# Invalid character 'A' in integer literal

**URL:** <https://discuss.hail.is/t/invalid-character-a-in-integer-literal/2329>\
**Category:** Hail Query & hailctl\
**Created:** [November 4, 2021, 8:48pm UTC](https://discuss.hail.is/t/invalid-character-a-in-integer-literal/2329 "2021-11-04T20:48:12Z")\
**Posts on this page:** 10\
**Page:** 1

<div class="post-metadata">

**Author:** ![Balazs](https://avatars.discourse-cdn.com/v4/letter/b/cc9497/32.png) [@Balazs](https://discuss.hail.is/u/Balazs)\
**Post date:** [November 4, 2021, 8:48pm UTC](https://discuss.hail.is/t/invalid-character-a-in-integer-literal/2329/1 "2021-11-04T20:48:12Z")

</div>

Hi all,

I run into this error when I tried to write out a newly annotated matrix table after I joined the dosage files to the genotype data (dosage files are from Tractor).

Hail version: 0.2.78-b17627756568  
Error summary: MatrixParseError: file:/Users/Tractor/chr22-1.anc2.hapcount.txt:28-29, invalid character ‘A’ in integer literal

---

<div class="post-metadata">

**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\
**Post date:** [November 4, 2021, 8:49pm UTC](https://discuss.hail.is/t/invalid-character-a-in-integer-literal/2329/2 "2021-11-04T20:49:22Z")

</div>

Hail’s lazy execution model means that this error is actually a problem with the _import_, not the write. Can you paste the full exception trace?

---

<div class="post-metadata">

**Author:** ![Balazs](https://avatars.discourse-cdn.com/v4/letter/b/cc9497/32.png) [@Balazs](https://discuss.hail.is/u/Balazs)\
**Post date:** [November 4, 2021, 8:56pm UTC](https://discuss.hail.is/t/invalid-character-a-in-integer-literal/2329/3 "2021-11-04T20:56:03Z")

</div>

## 2021-11-04 14:52:14 Hail: INFO: Coerced sorted dataset 2021-11-04 14:52:15 Hail: INFO: Coerced sorted dataset

FatalError Traceback (most recent call last)  
 in   
1 #write out the newly annotated matrix table. Will run a lot faster if we load this in again after annotating things in due to Hail processing style.  
----\> 2 mt.write(‘/Users/balazsmurnyak/Desktop/Tractor/new\_hail\_matrix.mt’)

in write(self, output, overwrite, stage\_locally, \_codec\_spec, \_partitions, \_checkpoint\_file)

~/opt/anaconda3/lib/python3.8/site-packages/hail/typecheck/check.py in wrapper(\_\_original\_func, \*args, \*\*kwargs)  
575 def wrapper(_original\_func, \*args, \*\*kwargs):  
576 args, kwargs_ = check\_all(\_\_original\_func, args, kwargs, checkers, is\_method=is\_method)  
 → 577 return _original\_func(\*args, \*\*kwargs_)  
578  
579 return wrapper

~/opt/anaconda3/lib/python3.8/site-packages/hail/matrixtable.py in write(self, output, overwrite, stage\_locally, \_codec\_spec, \_partitions, \_checkpoint\_file)  
2542  
2543 writer = ir.MatrixNativeWriter(output, overwrite, stage\_locally, \_codec\_spec, \_partitions, \_partitions\_type, \_checkpoint\_file)  
 → 2544 Env.backend().execute(ir.MatrixWrite(self.\_mir, writer))  
2545  
2546 class \_Show:

~/opt/anaconda3/lib/python3.8/site-packages/hail/backend/py4j\_backend.py in execute(self, ir, timed)  
108 raise HailUserError(message\_and\_trace) from None  
109  
 → 110 raise e

~/opt/anaconda3/lib/python3.8/site-packages/hail/backend/py4j\_backend.py in execute(self, ir, timed)  
84 # print(self.\_hail\_package.expr.ir.Pretty.apply(jir, True, -1))  
85 try:  
—\> 86 result\_tuple = self.\_jhc.backend().executeEncode(jir, stream\_codec)  
87 (result, timings) = (result\_tuple.\_1(), result\_tuple.\_2())  
88 value = ir.typ.\_from\_encoding(result)

~/opt/anaconda3/lib/python3.8/site-packages/py4j/java\_gateway.py in **call** (self, \*args)  
1302  
1303 answer = self.gateway\_client.send\_command(command)  
 → 1304 return\_value = get\_return\_value(  
1305 answer, self.gateway\_client, self.target\_id, self.name)  
1306

~/opt/anaconda3/lib/python3.8/site-packages/hail/backend/py4j\_backend.py in deco(\*args, \*\*kwargs)  
27 raise FatalError(‘Error summary: %s’ % (deepest,), error\_id) from None  
28 else:  
—\> 29 raise FatalError(‘%s\n\nJava stack trace:\n%s\n’  
30 ‘Hail version: %s\n’  
31 ‘Error summary: %s’ % (deepest, full, hail. **version** , deepest), error\_id) from None

FatalError: MatrixParseError: file:/Users/balazsmurnyak/Desktop/Tractor/Oall\_GT\_R2\_.5\_MAF\_.001\_chr22-1.anc2.hapcount.txt:28-29, invalid character ‘C’ in integer literal

Java stack trace:  
org.apache.spark.SparkException: Job aborted due to stage failure: Task 24 in stage 9.0 failed 1 times, most recent failure: Lost task 24.0 in stage 9.0 (TID 249) (10.16.191.97 executor driver): is.hail.utils.HailException: ""Error parse line 2:28-29:  
File: file:/Users/balazsmurnyak/Desktop/Tractor/Oall\_GT\_R2\_.5\_MAF\_.001\_chr22-1.anc2.hapcount.txt  
Line:  
22 17070764 22:17070764:C:G C G 0 0 0 0 0 0 0 0 0 0 0 0 0 0 …  
at is.hail.utils.ErrorHandling.fatal(ErrorHandling.scala:15)  
at is.hail.utils.ErrorHandling.fatal$(ErrorHandling.scala:15)  
at is.hail.utils.package$.fatal(package.scala:78)  
at is.hail.io.CompiledLineParser.$anonfun$apply$1(TextMatrixReader.scala:691)  
at is.hail.io.CompiledLineParser.$anonfun$apply$1$adapted(TextMatrixReader.scala:673)  
at scala.collection.Iterator$$anon$10.next(Iterator.scala:459)  
at \_\_C1468stream.apply\_region5\_75(Unknown Source)  
at _C1468stream.apply(Unknown Source)  
at is.hail.expr.ir.CompileIterator$$anon$2.step(Compile.scala:312)  
at is.hail.expr.ir.CompileIterator$LongIteratorWrapper.hasNext(Compile.scala:168)  
at scala.collection.Iterator$$anon$10.hasNext(Iterator.scala:458)  
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:488)  
at scala.collection.Iterator$$anon$10.hasNext(Iterator.scala:458)  
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:488)  
at is.hail.rvd.RVD$.$anonfun$getKeyInfo$2(RVD.scala:1232)  
at is.hail.rvd.RVD$.$anonfun$getKeyInfo$2$adapted(RVD.scala:1231)  
at is.hail.sparkextras.ContextRDD.$anonfun$crunJobWithIndex$1(ContextRDD.scala:242)  
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)  
at org.apache.spark.scheduler.Task.run(Task.scala:131)  
at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$3(Executor.scala:497)  
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1439)  
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:500)  
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)  
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)  
at java.lang.Thread.run(Thread.java:748)  
Caused by: is.hail.io.MatrixParseError: file:/Users/balazsmurnyak/Desktop/Tractor/Oall\_GT\_R2.5\_MAF_.001\_chr22-1.anc2.hapcount.txt:28-29, invalid character ‘C’ in integer literal  
at \_\_C1505text\_matrix\_reader.\_\_m1511parseInt(Unknown Source)  
at \_\_C1505text\_matrix\_reader.apply\_region8\_51(Unknown Source)  
at \_\_C1505text\_matrix\_reader.apply(Unknown Source)  
at \_\_C1505text\_matrix\_reader.apply(Unknown Source)  
at is.hail.io.CompiledLineParser.$anonfun$apply$1(TextMatrixReader.scala:681)  
… 21 more

Driver stacktrace:  
at org.apache.spark.scheduler.DAGScheduler.failJobAndIndependentStages(DAGScheduler.scala:2258)  
at org.apache.spark.scheduler.DAGScheduler.$anonfun$abortStage$2(DAGScheduler.scala:2207)  
at org.apache.spark.scheduler.DAGScheduler.$anonfun$abortStage$2$adapted(DAGScheduler.scala:2206)  
at scala.collection.mutable.ResizableArray.foreach(ResizableArray.scala:62)  
at scala.collection.mutable.ResizableArray.foreach$(ResizableArray.scala:55)  
at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:49)  
at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:2206)  
at org.apache.spark.scheduler.DAGScheduler.$anonfun$handleTaskSetFailed$1(DAGScheduler.scala:1079)  
at org.apache.spark.scheduler.DAGScheduler.$anonfun$handleTaskSetFailed$1$adapted(DAGScheduler.scala:1079)  
at scala.Option.foreach(Option.scala:407)  
at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:1079)  
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:2445)  
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2387)  
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:2376)  
at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:49)  
at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:868)  
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2196)  
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2217)  
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2249)  
at is.hail.sparkextras.ContextRDD.crunJobWithIndex(ContextRDD.scala:238)  
at is.hail.rvd.RVD$.getKeyInfo(RVD.scala:1231)  
at is.hail.rvd.RVD$.makeCoercer(RVD.scala:1306)  
at is.hail.rvd.RVD$.coerce(RVD.scala:1262)  
at is.hail.rvd.RVD.changeKey(RVD.scala:143)  
at is.hail.rvd.RVD.changeKey(RVD.scala:136)  
at is.hail.backend.spark.SparkBackend.lowerDistributedSort(SparkBackend.scala:685)  
at is.hail.expr.ir.lowering.LowerTableIR$.lower$1(LowerTableIR.scala:975)  
at is.hail.expr.ir.lowering.LowerTableIR$.lower$1(LowerTableIR.scala:986)  
at is.hail.expr.ir.lowering.LowerTableIR$.lower$1(LowerTableIR.scala:475)  
at is.hail.expr.ir.lowering.LowerTableIR$.lower$1(LowerTableIR.scala:857)  
at is.hail.expr.ir.lowering.LowerTableIR$.lower$1(LowerTableIR.scala:475)  
at is.hail.expr.ir.lowering.LowerTableIR$.lower$1(LowerTableIR.scala:857)  
at is.hail.expr.ir.lowering.LowerTableIR$.lower$1(LowerTableIR.scala:475)  
at is.hail.expr.ir.lowering.LowerTableIR$.lower$1(LowerTableIR.scala:857)  
at is.hail.expr.ir.lowering.LowerTableIR$.lower$1(LowerTableIR.scala:475)  
at is.hail.expr.ir.lowering.LowerTableIR$.apply(LowerTableIR.scala:1333)  
at is.hail.expr.ir.lowering.LowerToCDA$.lower(LowerToCDA.scala:69)  
at is.hail.expr.ir.lowering.LowerToCDA$.apply(LowerToCDA.scala:18)  
at is.hail.expr.ir.lowering.LowerToDistributedArrayPass.transform(LoweringPass.scala:77)  
at is.hail.expr.ir.LowerOrInterpretNonCompilable$.evaluate$1(LowerOrInterpretNonCompilable.scala:27)  
at is.hail.expr.ir.LowerOrInterpretNonCompilable$.rewrite$1(LowerOrInterpretNonCompilable.scala:67)  
at is.hail.expr.ir.LowerOrInterpretNonCompilable$.apply(LowerOrInterpretNonCompilable.scala:72)  
at is.hail.expr.ir.lowering.LowerOrInterpretNonCompilablePass$.transform(LoweringPass.scala:69)  
at is.hail.expr.ir.lowering.LoweringPass.$anonfun$apply$3(LoweringPass.scala:16)  
at is.hail.utils.ExecutionTimer.time(ExecutionTimer.scala:81)  
at is.hail.expr.ir.lowering.LoweringPass.$anonfun$apply$1(LoweringPass.scala:16)  
at is.hail.utils.ExecutionTimer.time(ExecutionTimer.scala:81)  
at is.hail.expr.ir.lowering.LoweringPass.apply(LoweringPass.scala:14)  
at is.hail.expr.ir.lowering.LoweringPass.apply$(LoweringPass.scala:13)  
at is.hail.expr.ir.lowering.LowerOrInterpretNonCompilablePass$.apply(LoweringPass.scala:64)  
at is.hail.expr.ir.lowering.LoweringPipeline.$anonfun$apply$1(LoweringPipeline.scala:15)  
at is.hail.expr.ir.lowering.LoweringPipeline.$anonfun$apply$1$adapted(LoweringPipeline.scala:13)  
at scala.collection.IndexedSeqOptimized.foreach(IndexedSeqOptimized.scala:36)  
at scala.collection.IndexedSeqOptimized.foreach$(IndexedSeqOptimized.scala:33)  
at scala.collection.mutable.WrappedArray.foreach(WrappedArray.scala:38)  
at is.hail.expr.ir.lowering.LoweringPipeline.apply(LoweringPipeline.scala:13)  
at is.hail.expr.ir.CompileAndEvaluate$.\_apply(CompileAndEvaluate.scala:47)  
at is.hail.backend.spark.SparkBackend.\_execute(SparkBackend.scala:381)  
at is.hail.backend.spark.SparkBackend.$anonfun$executeEncode$2(SparkBackend.scala:417)  
at is.hail.backend.ExecuteContext$.$anonfun$scoped$3(ExecuteContext.scala:47)  
at is.hail.utils.package$.using(package.scala:638)  
at is.hail.backend.ExecuteContext$.$anonfun$scoped$2(ExecuteContext.scala:47)  
at is.hail.utils.package$.using(package.scala:638)  
at is.hail.annotations.RegionPool$.scoped(RegionPool.scala:17)  
at is.hail.backend.ExecuteContext$.scoped(ExecuteContext.scala:46)  
at is.hail.backend.spark.SparkBackend.withExecuteContext(SparkBackend.scala:275)  
at is.hail.backend.spark.SparkBackend.$anonfun$executeEncode$1(SparkBackend.scala:414)  
at is.hail.utils.ExecutionTimer$.time(ExecutionTimer.scala:52)  
at is.hail.backend.spark.SparkBackend.executeEncode(SparkBackend.scala:413)  
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)  
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)  
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)  
at java.lang.reflect.Method.invoke(Method.java:498)  
at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)  
at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)  
at py4j.Gateway.invoke(Gateway.java:282)  
at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)  
at py4j.commands.CallCommand.execute(CallCommand.java:79)  
at py4j.GatewayConnection.run(GatewayConnection.java:238)  
at java.lang.Thread.run(Thread.java:748)

is.hail.utils.HailException: ""Error parse line 2:28-29:  
File: file:/Users/balazsmurnyak/Desktop/Tractor/Oall\_GT\_R2\_.5\_MAF\_.001\_chr22-1.anc2.hapcount.txt  
Line:  
22 17070764 22:17070764:C:G C G 0 0 0 0 0 0 0 0 0 0 0 0 0 0 …  
at is.hail.utils.ErrorHandling.fatal(ErrorHandling.scala:15)  
at is.hail.utils.ErrorHandling.fatal$(ErrorHandling.scala:15)  
at is.hail.utils.package$.fatal(package.scala:78)  
at is.hail.io.CompiledLineParser.$anonfun$apply$1(TextMatrixReader.scala:691)  
at is.hail.io.CompiledLineParser.$anonfun$apply$1$adapted(TextMatrixReader.scala:673)  
at scala.collection.Iterator$$anon$10.next(Iterator.scala:459)  
at \_\_C1468stream.apply\_region5\_75(Unknown Source)  
at \_\_C1468stream.apply(Unknown Source)  
at is.hail.expr.ir.CompileIterator$$anon$2.step(Compile.scala:312)  
at is.hail.expr.ir.CompileIterator$LongIteratorWrapper.hasNext(Compile.scala:168)  
at scala.collection.Iterator$$anon$10.hasNext(Iterator.scala:458)  
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:488)  
at scala.collection.Iterator$$anon$10.hasNext(Iterator.scala:458)  
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:488)  
at is.hail.rvd.RVD$.$anonfun$getKeyInfo$2(RVD.scala:1232)  
at is.hail.rvd.RVD$.$anonfun$getKeyInfo$2$adapted(RVD.scala:1231)  
at is.hail.sparkextras.ContextRDD.$anonfun$crunJobWithIndex$1(ContextRDD.scala:242)  
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)  
at org.apache.spark.scheduler.Task.run(Task.scala:131)  
at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$3(Executor.scala:497)  
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1439)  
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:500)  
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)  
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)  
at java.lang.Thread.run(Thread.java:748)

is.hail.io.MatrixParseError: file:/Users/balazsmurnyak/Desktop/Tractor/Oall\_GT\_R2\_.5\_MAF\_.001\_chr22-1.anc2.hapcount.txt:28-29, invalid character ‘C’ in integer literal  
at \_\_C1505text\_matrix\_reader.\_\_m1511parseInt(Unknown Source)  
at \_\_C1505text\_matrix\_reader.apply\_region8\_51(Unknown Source)  
at \_\_C1505text\_matrix\_reader.apply(Unknown Source)  
at \_\_C1505text\_matrix\_reader.apply(Unknown Source)  
at is.hail.io.CompiledLineParser.$anonfun$apply$1(TextMatrixReader.scala:681)  
at is.hail.io.CompiledLineParser.$anonfun$apply$1$adapted(TextMatrixReader.scala:673)  
at scala.collection.Iterator$$anon$10.next(Iterator.scala:459)  
at \_\_C1468stream.apply\_region5\_75(Unknown Source)  
at \_\_C1468stream.apply(Unknown Source)  
at is.hail.expr.ir.CompileIterator$$anon$2.step(Compile.scala:312)  
at is.hail.expr.ir.CompileIterator$LongIteratorWrapper.hasNext(Compile.scala:168)  
at scala.collection.Iterator$$anon$10.hasNext(Iterator.scala:458)  
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:488)  
at scala.collection.Iterator$$anon$10.hasNext(Iterator.scala:458)  
at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:488)  
at is.hail.rvd.RVD$.$anonfun$getKeyInfo$2(RVD.scala:1232)  
at is.hail.rvd.RVD$.$anonfun$getKeyInfo$2$adapted(RVD.scala:1231)  
at is.hail.sparkextras.ContextRDD.$anonfun$crunJobWithIndex$1(ContextRDD.scala:242)  
at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:90)  
at org.apache.spark.scheduler.Task.run(Task.scala:131)  
at org.apache.spark.executor.Executor$TaskRunner.$anonfun$run$3(Executor.scala:497)  
at org.apache.spark.util.Utils$.tryWithSafeFinally(Utils.scala:1439)  
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:500)  
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)  
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)  
at java.lang.Thread.run(Thread.java:748)

Hail version: 0.2.78-b17627756568  
Error summary: MatrixParseError: file:/Users/balazsmurnyak/Desktop/Tractor/Oall\_GT\_R2\_.5\_MAF\_.001\_chr22-1.anc2.hapcount.txt:28-29, invalid character ‘C’ in integer literal

---

<div class="post-metadata">

**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\
**Post date:** [November 4, 2021, 8:59pm UTC](https://discuss.hail.is/t/invalid-character-a-in-integer-literal/2329/4 "2021-11-04T20:59:50Z")

</div>

This error says that one of those ‘C’ fields is trying to be read as an int. I think this is because the import command didn’t get the right set of row fields to indicate that certain fields are not matrix columns. What’s the import command you used?

---

<div class="post-metadata">

**Author:** ![Balazs](https://avatars.discourse-cdn.com/v4/letter/b/cc9497/32.png) [@Balazs](https://discuss.hail.is/u/Balazs)\
**Post date:** [November 4, 2021, 9:10pm UTC](https://discuss.hail.is/t/invalid-character-a-in-integer-literal/2329/5 "2021-11-04T21:10:23Z")

</div>

I used the " hl.import\_matrix\_table " command

row\_fields={‘CHROM’: hl.tstr, ‘POS’: hl.tint, ‘ID’: hl.tstr}  
hapcounts0 = hl.import\_matrix\_table(’/Users/balazsmurnyak/Desktop/Tractor/Oall\_GT\_R2\_.5\_MAF\_.001\_chr22-1.anc2.hapcount.txt.gz’,  
force\_bgz=True, row\_fields=row\_fields, row\_key=[], min\_partitions=32)  
hapcounts0 = hapcounts0.key\_rows\_by().drop(‘row\_id’)  
hapcounts0 = hapcounts0.key\_rows\_by(locus=hl.locus(hapcounts0.CHROM, hapcounts0.POS))

---

<div class="post-metadata">

**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\
**Post date:** [November 4, 2021, 9:11pm UTC](https://discuss.hail.is/t/invalid-character-a-in-integer-literal/2329/6 "2021-11-04T21:11:11Z")

</div>

What’s the first line of the file?  
I think there are some other allele fields that need to be included in row\_fields.

---

<div class="post-metadata">

**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\
**Post date:** [November 4, 2021, 9:11pm UTC](https://discuss.hail.is/t/invalid-character-a-in-integer-literal/2329/7 "2021-11-04T21:11:28Z")

</div>

(at least what’s the first line up to the sample IDs)

---

<div class="post-metadata">

**Author:** ![Balazs](https://avatars.discourse-cdn.com/v4/letter/b/cc9497/32.png) [@Balazs](https://discuss.hail.is/u/Balazs)\
**Post date:** [November 4, 2021, 9:18pm UTC](https://discuss.hail.is/t/invalid-character-a-in-integer-literal/2329/8 "2021-11-04T21:18:36Z")

</div>

import argparse  
import hail as hl  
import numpy as np  
hl.init()

from hail.plot import show  
from pprint import pprint  
hl.plot.output\_notebook()

mt = hl.import\_vcf(’/Users/balazsmurnyak/Desktop/Tractor/Oall\_GT\_R2\_.5\_MAF\_.001\_chr22-1.anc2.vcf’).key\_rows\_by(‘locus’)

row\_fields={‘CHROM’: hl.tstr, ‘POS’: hl.tint, ‘ID’: hl.tstr, ‘REF’: hl.tstr, ‘ALT’: hl.tstr}  
anc0dos = hl.import\_matrix\_table(’/Users/balazsmurnyak/Desktop/Tractor/Oall\_GT\_R2\_.5\_MAF\_.001\_chr22-1.anc2.dosage.txt’,  
force\_bgz=True, row\_fields=row\_fields, row\_key=[], min\_partitions=32)  
anc0dos = anc0dos.key\_rows\_by().drop(‘row\_id’)  
anc0dos = anc0dos.key\_rows\_by(locus=hl.locus(anc0dos.CHROM, anc0dos.POS))

row\_fields={‘CHROM’: hl.tstr, ‘POS’: hl.tint, ‘ID’: hl.tstr}  
hapcounts0 = hl.import\_matrix\_table(’/Users/balazsmurnyak/Desktop/Tractor/Oall\_GT\_R2\_.5\_MAF\_.001\_chr22-1.anc2.hapcount.txt’,  
force\_bgz=True, row\_fields=row\_fields, row\_key=[], min\_partitions=32)  
hapcounts0 = hapcounts0.key\_rows\_by().drop(‘row\_id’)  
hapcounts0 = hapcounts0.key\_rows\_by(locus=hl.locus(hapcounts0.CHROM, hapcounts0.POS))

mt = mt.annotate\_entries(anc0dos = anc0dos[mt.locus, mt.s], hapcounts0 = hapcounts0[mt.locus, mt.s])  
mt.write(’/Users/balazsmurnyak/Desktop/Tractor/new\_hail\_matrix.mt’)

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<div class="post-metadata">

**Author:** ![tpoterba](https://yyz2.discourse-cdn.com/flex036/user_avatar/discuss.hail.is/tpoterba/32/61_2.png) [@tpoterba](https://discuss.hail.is/u/tpoterba)\
**Post date:** [November 5, 2021, 8:53pm UTC](https://discuss.hail.is/t/invalid-character-a-in-integer-literal/2329/9 "2021-11-05T20:53:15Z")

</div>

Don’t you need the `REF` and `ALT` fields for the second file?

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<div class="post-metadata">

**Author:** ![Balazs](https://avatars.discourse-cdn.com/v4/letter/b/cc9497/32.png) [@Balazs](https://discuss.hail.is/u/Balazs)\
**Post date:** [November 8, 2021, 4:46pm UTC](https://discuss.hail.is/t/invalid-character-a-in-integer-literal/2329/10 "2021-11-08T16:46:15Z")

</div>

Yes, exactly! Now it works. Thanks for your help!