There is no final output

[wjq1981]

#1
docker run -it --rm -v${WORKING_DIR}:${WORKING_DIR} dockerpull.org/mobinasri/flagger:v1.1.0 \

    bam2cov --bam ${WORKING_DIR}/hifi.mapsort.bam \
            --output ${WORKING_DIR}/coverage_file.cov.gz \
            --annotationJson ${WORKING_DIR}/annotations_path.json \
            --threads 8 \
            --baselineAnnotation whole_genome

[2024-12-30 15:52:55] Created thread for parsing batch 0 (length=45704987)
[2024-12-30 15:52:55] Created thread for parsing batch 1 (length=45704987)
[2024-12-30 15:52:55] Created thread for parsing batch 2 (length=45704987)
[2024-12-30 15:52:55] Created thread for parsing batch 3 (length=45704987)
[2024-12-30 15:52:55] Created thread for parsing batch 4 (length=45704987)
[2024-12-30 15:52:55] Created thread for parsing batch 5 (length=45704987)
[2024-12-30 15:52:55] Created thread for parsing batch 6 (length=45704987)
[2024-12-30 15:52:55] Created thread for parsing batch 7 (length=45704987)
[2024-12-30 15:52:55] Started parsing reads in the block: 6 0 2346016
[2024-12-30 15:52:55] Started parsing reads in the block: 10 0 6434832
[2024-12-30 15:52:55] Started parsing reads in the block: 14 9124924 17264678
[2024-12-30 15:52:55] Started parsing reads in the block: 14 0 9124924
[2024-12-30 15:52:55] Started parsing reads in the block: 2 20660261 30864380
[2024-12-30 15:52:55] Started parsing reads in the block: 11 0 22486397
[2024-12-30 15:52:55] Started parsing reads in the block: 8 0 318348
[2024-12-30 15:52:55] Started parsing reads in the block: 9 0 22780935
[2024-12-30 15:52:56] Started parsing reads in the block: 6 2346016 23913987
[2024-12-30 15:53:01] Started parsing reads in the block: 4 7977551 26917655
[2024-12-30 15:53:07] Started parsing reads in the block: 1 0 39270155
[2024-12-30 15:53:13] Started parsing reads in the block: 3 0 27523317
[2024-12-30 15:53:13] Started parsing reads in the block: 12 7030765 22466537
[2024-12-30 15:53:15] Started parsing reads in the block: 2 0 20660261
[2024-12-30 15:53:25][4:7977551-26917655] Parsed 100000 reads.
[2024-12-30 15:53:25][6:2346016-23913987] Parsed 100000 reads.
[2024-12-30 15:53:27][12:7030765-22466537] Parsed 100000 reads.
[2024-12-30 15:53:29][1:0-39270155] Parsed 100000 reads.
[2024-12-30 15:53:29][9:0-22780935] Parsed 100000 reads.
[2024-12-30 15:53:30][3:0-27523317] Parsed 100000 reads.
[2024-12-30 15:53:31][2:0-20660261] Parsed 100000 reads.
[2024-12-30 15:53:33][11:0-22486397] Parsed 100000 reads.
[2024-12-30 15:53:36] Started parsing reads in the block: 5 0 24418867
[2024-12-30 15:53:42] Started parsing reads in the block: 7 0 23818668
[2024-12-30 15:53:42] Started parsing reads in the block: 8 318348 23242400
[2024-12-30 15:53:48] Started parsing reads in the block: 12 0 7030765
[2024-12-30 15:53:51] Started parsing reads in the block: 13 0 21144291
[2024-12-30 15:53:59][7:0-23818668] Parsed 200000 reads.
[2024-12-30 15:54:00][5:0-24418867] Parsed 200000 reads.
[2024-12-30 15:54:00][3:0-27523317] Parsed 200000 reads.
[2024-12-30 15:54:01] Started parsing reads in the block: 10 6434832 22622657
[2024-12-30 15:54:02][13:0-21144291] Parsed 200000 reads.
[2024-12-30 15:54:05][2:0-20660261] Parsed 200000 reads.
[2024-12-30 15:54:07][10:6434832-22622657] Parsed 200000 reads.
[2024-12-30 15:54:08] Started parsing reads in the block: 4 0 7977551
[2024-12-30 15:54:09][8:318348-23242400] Parsed 200000 reads.
[2024-12-30 15:54:11] Started parsing reads in the block: 15 0 16904972
[2024-12-30 15:54:12][1:0-39270155] Parsed 200000 reads.
[2024-12-30 15:54:25][5:0-24418867] Parsed 300000 reads.
[2024-12-30 15:54:40][15:0-16904972] Parsed 300000 reads.
[2024-12-30 15:54:58] All batches are parsed.
[2024-12-30 15:54:58] Started sorting and merging blocks.
[2024-12-30 15:57:02] Merging coverage blocks is done.
[2024-12-30 15:57:03] Created block table with coverage data : tot_len=365638297, number=4169182
[2024-12-30 15:57:03] Created block table for whole genome : tot_len=365639896, number=15
{
"whole_genome" : "Geno-s.bed"
}
[2024-12-30 15:57:03] Parsed annotation whole_genome:Geno-s.bed
[2024-12-30 15:57:03] Number of created annotation block tables = 2
[2024-12-30 15:57:03] Added annotation blocks to coverage block tables: tot_len=1096918089, number=4169212
[2024-12-30 15:57:03] Started sorting and merging blocks
[2024-12-30 15:57:04] Blocks before merging : tot_len=1096918089, number=4169212
[2024-12-30 15:57:04] Created final block table : tot_len=365639896, number=4169185
{
"whole_genome" : "Geno-s.bed"
}
[2024-12-30 15:57:05] Number of annotations added to the blocks table (+1 for 'no_annotation' which is a reserved annotation name for blocks with no annotation): 2
[2024-12-30 15:57:05] Bias detection is disabled. Running bias module only for getting the whole genome median coverage.
[2024-12-30 15:57:05] Whole genome median coverage = 103
[2024-12-30 15:57:09] Started writing to coverage_file.cov.gz.
[2024-12-30 15:57:17] Done.
Real time: 262.047 sec; CPU: 1124.209 sec; Peak RSS: 1.849 GB; CPU usage: 429.0%

#2
mkdir -p ${WORKING_DIR}/hmm_flagger_outputs
docker run -it --rm -v${WORKING_DIR}:${WORKING_DIR} dockerpull.org/mobinasri/flagger:v1.1.0 \

    hmm_flagger \
           --input ${WORKING_DIR}/coverage_file.cov.gz \
           --outputDir ${WORKING_DIR}/hmm_flagger_outputs  \
           --alphaTsv alpha_optimum_trunc_exp_gaussian_w_16000_n_50.HiFi_DC_1.2_DEC_2024.v1.1.0.tsv \
           --labelNames Err,Dup,Hap,Col \
           --threads 8

[2024-12-30 16:05:46] Parsing/Creating coverage chunks.
[2024-12-30 16:05:46] The given input file is not binary so chunks will be constructed from cov file.
[2024-12-30 16:05:46] Index file does not exist: expected path coverage_file.cov.gz.index
[2024-12-30 16:05:46] Constructing index in memory ...
[2024-12-30 16:05:50] Index is constructed.
[2024-12-30 16:05:50] Index file (coverage_file.cov.gz.index) is written
[2024-12-30 16:05:50] Index is saved into coverage_file.cov.gz.index (It will skip index construction for next runs).
[2024-12-30 16:05:50] Parsing header info for ChunksCreator.
[2024-12-30 16:05:51] Truth tag was set to false (or not defined) so truth labels will not be parsed from file.
[2024-12-30 16:05:51] Prediction tag was set to false (or not defined) so prediction labels will not be parsed from file.
[2024-12-30 16:05:51] Creating empty chunks.
[2024-12-30 16:05:51] Created a thread pool with 8 threads for parsing chunks
[2024-12-30 16:05:51] Queued 15 jobs for the thread pool (no more than 8 jobs will be processed at a time)
[2024-12-30 16:06:09] Chunks are constructed from cov file.
[2024-12-30 16:06:09] 15 chunks are parsed covering total length of 365639896 bases.
[2024-12-30 16:06:09] Determining the number of components for the 'collapsed' state.
[2024-12-30 16:06:09] The number of collapsed components (n=3) is determined and adjusted automatically by taking the maximum observed coverage.
[2024-12-30 16:06:09] Creating HMM model.

Hi, here is my code with runtime output. I observed that no errors are reported during the run, but the results are not generated by the 'prediction_summary_final.tsv' file. Can you help me to see why?

[mobinasri]

Hi @wjq1981 Thanks for reporting this. Could you please share the cov.gz file so that I can take a look?

[wjq1981]

Hi @mobinasri . The file is over 50 megabytes and github won't upload it, do you have any ideas?

[mobinasri]

Hi @mobinasri . The file is over 50 megabytes and github won't upload it, do you have any ideas?

Google Drive is one option.

[wjq1981]

Hi @mobinasri . The file is over 50 megabytes and github won't upload it, do you have any ideas?

Google Drive is one option.

https://drive.google.com/file/d/1yhA1qhfDWGVBc1woGfCjevI23PDwl1MD/view?usp=sharing

[wjq1981]

Hi @mobinasri .Did you get the file? What was the reason it reported an error?

[mobinasri]

Hi @wjq1981 I guess I realized why you don't get the outputs. It is because the path to alpha tsv file is not given correctly. Please add ${WORKING_DIR}/ if that's available in your working directory.

docker run -it --rm -v${WORKING_DIR}:${WORKING_DIR} dockerpull.org/mobinasri/flagger:v1.1.0 \
  hmm_flagger \
         --input ${WORKING_DIR}/coverage_file.cov.gz \
         --outputDir ${WORKING_DIR}/hmm_flagger_outputs  \
         --alphaTsv ${WORKING_DIR}/alpha_optimum_trunc_exp_gaussian_w_16000_n_50.HiFi_DC_1.2_DEC_2024.v1.1.0.tsv \
         --labelNames Err,Dup,Hap,Col \
         --threads 8

[wjq1981]

Hi @mobinasri . Thank you very much, this issue has been resolved.