Job ID = 6497576 SRX = SRX747302 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:26:52 prefetch.2.10.7: 1) Downloading 'SRR1635000'... 2020-06-25T22:26:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:28:29 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:28:29 prefetch.2.10.7: 'SRR1635000' is valid 2020-06-25T22:28:29 prefetch.2.10.7: 1) 'SRR1635000' was downloaded successfully 2020-06-25T22:29:02 prefetch.2.10.7: 'SRR1635000' has 6 unresolved dependencies 2020-06-25T22:29:02 prefetch.2.10.7: 2) Downloading 'ncbi-acc:BX284601.4?vdb-ctx=refseq'... 2020-06-25T22:29:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:35:53 prefetch.2.10.7: HTTPS download failed 2020-06-25T22:35:53 prefetch.2.10.7: 2) failed to download ncbi-acc:BX284601.4?vdb-ctx=refseq 2020-06-25T22:55:28 fastq-dump.2.10.7 err: transfer canceled while allocating buffer within file system module - Cannot KHttpFileTimedReadChunked: to=60 2020-06-25T22:55:28 fastq-dump.2.10.7 err: data corrupt while selecting function within transform module - failed SRR1635000/SRR1635000.sra ============================================================= An error occurred during processing. A report was generated into the file '/home/okishinya/ncbi_error_report.txt'. If the problem persists, you may consider sending the file to 'sra-tools@ncbi.nlm.nih.gov' for assistance. ============================================================= fastq-dump quit with error code 3 fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:01 15353856 reads; of these: 15353856 (100.00%) were unpaired; of these: 75927 (0.49%) aligned 0 times 13337354 (86.87%) aligned exactly 1 time 1940575 (12.64%) aligned >1 times 99.51% overall alignment rate Time searching: 00:02:01 Overall time: 00:02:01 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 3409001 / 15277929 = 0.2231 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 08:00:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX747302/SRX747302.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX747302/SRX747302.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX747302/SRX747302.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX747302/SRX747302.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 26 Jun 2020 08:00:56: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:00:56: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:01:01: 1000000 INFO @ Fri, 26 Jun 2020 08:01:06: 2000000 INFO @ Fri, 26 Jun 2020 08:01:11: 3000000 INFO @ Fri, 26 Jun 2020 08:01:16: 4000000 INFO @ Fri, 26 Jun 2020 08:01:20: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 08:01:25: 6000000 INFO @ Fri, 26 Jun 2020 08:01:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX747302/SRX747302.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX747302/SRX747302.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX747302/SRX747302.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX747302/SRX747302.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 26 Jun 2020 08:01:26: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:01:26: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:01:31: 7000000 INFO @ Fri, 26 Jun 2020 08:01:31: 1000000 INFO @ Fri, 26 Jun 2020 08:01:36: 8000000 INFO @ Fri, 26 Jun 2020 08:01:36: 2000000 INFO @ Fri, 26 Jun 2020 08:01:41: 9000000 INFO @ Fri, 26 Jun 2020 08:01:41: 3000000 INFO @ Fri, 26 Jun 2020 08:01:46: 10000000 INFO @ Fri, 26 Jun 2020 08:01:47: 4000000 INFO @ Fri, 26 Jun 2020 08:01:51: 11000000 INFO @ Fri, 26 Jun 2020 08:01:52: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 08:01:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX747302/SRX747302.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX747302/SRX747302.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX747302/SRX747302.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX747302/SRX747302.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 26 Jun 2020 08:01:56: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:01:56: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:01:56: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 08:01:56: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 08:01:56: #1 total tags in treatment: 11868928 INFO @ Fri, 26 Jun 2020 08:01:56: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:01:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:01:56: #1 tags after filtering in treatment: 11868928 INFO @ Fri, 26 Jun 2020 08:01:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:01:56: #1 finished! INFO @ Fri, 26 Jun 2020 08:01:56: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:01:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:01:57: #2 number of paired peaks: 428 WARNING @ Fri, 26 Jun 2020 08:01:57: Fewer paired peaks (428) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 428 pairs to build model! INFO @ Fri, 26 Jun 2020 08:01:57: start model_add_line... INFO @ Fri, 26 Jun 2020 08:01:57: start X-correlation... INFO @ Fri, 26 Jun 2020 08:01:57: end of X-cor INFO @ Fri, 26 Jun 2020 08:01:57: #2 finished! INFO @ Fri, 26 Jun 2020 08:01:57: #2 predicted fragment length is 158 bps INFO @ Fri, 26 Jun 2020 08:01:57: #2 alternative fragment length(s) may be 4,158 bps INFO @ Fri, 26 Jun 2020 08:01:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX747302/SRX747302.05_model.r INFO @ Fri, 26 Jun 2020 08:01:57: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:01:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:01:57: 6000000 INFO @ Fri, 26 Jun 2020 08:02:02: 1000000 INFO @ Fri, 26 Jun 2020 08:02:03: 7000000 INFO @ Fri, 26 Jun 2020 08:02:07: 2000000 INFO @ Fri, 26 Jun 2020 08:02:08: 8000000 INFO @ Fri, 26 Jun 2020 08:02:13: 9000000 INFO @ Fri, 26 Jun 2020 08:02:13: 3000000 INFO @ Fri, 26 Jun 2020 08:02:19: 10000000 INFO @ Fri, 26 Jun 2020 08:02:19: 4000000 INFO @ Fri, 26 Jun 2020 08:02:24: 11000000 INFO @ Fri, 26 Jun 2020 08:02:25: 5000000 INFO @ Fri, 26 Jun 2020 08:02:27: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:02:29: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 08:02:29: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 08:02:29: #1 total tags in treatment: 11868928 INFO @ Fri, 26 Jun 2020 08:02:29: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:02:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:02:29: #1 tags after filtering in treatment: 11868928 INFO @ Fri, 26 Jun 2020 08:02:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:02:29: #1 finished! INFO @ Fri, 26 Jun 2020 08:02:29: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:02:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:02:30: #2 number of paired peaks: 428 WARNING @ Fri, 26 Jun 2020 08:02:30: Fewer paired peaks (428) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 428 pairs to build model! INFO @ Fri, 26 Jun 2020 08:02:30: start model_add_line... INFO @ Fri, 26 Jun 2020 08:02:30: start X-correlation... INFO @ Fri, 26 Jun 2020 08:02:30: end of X-cor INFO @ Fri, 26 Jun 2020 08:02:30: #2 finished! INFO @ Fri, 26 Jun 2020 08:02:30: #2 predicted fragment length is 158 bps INFO @ Fri, 26 Jun 2020 08:02:30: #2 alternative fragment length(s) may be 4,158 bps INFO @ Fri, 26 Jun 2020 08:02:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX747302/SRX747302.10_model.r INFO @ Fri, 26 Jun 2020 08:02:30: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:02:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:02:31: 6000000 INFO @ Fri, 26 Jun 2020 08:02:37: 7000000 INFO @ Fri, 26 Jun 2020 08:02:42: 8000000 INFO @ Fri, 26 Jun 2020 08:02:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX747302/SRX747302.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:02:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX747302/SRX747302.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:02:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX747302/SRX747302.05_summits.bed INFO @ Fri, 26 Jun 2020 08:02:44: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (8791 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:02:47: 9000000 INFO @ Fri, 26 Jun 2020 08:02:53: 10000000 INFO @ Fri, 26 Jun 2020 08:02:58: 11000000 INFO @ Fri, 26 Jun 2020 08:02:59: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:03:03: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 08:03:03: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 08:03:03: #1 total tags in treatment: 11868928 INFO @ Fri, 26 Jun 2020 08:03:03: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:03:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:03:03: #1 tags after filtering in treatment: 11868928 INFO @ Fri, 26 Jun 2020 08:03:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:03:03: #1 finished! INFO @ Fri, 26 Jun 2020 08:03:03: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:03:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:03:04: #2 number of paired peaks: 428 WARNING @ Fri, 26 Jun 2020 08:03:04: Fewer paired peaks (428) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 428 pairs to build model! INFO @ Fri, 26 Jun 2020 08:03:04: start model_add_line... INFO @ Fri, 26 Jun 2020 08:03:04: start X-correlation... INFO @ Fri, 26 Jun 2020 08:03:04: end of X-cor INFO @ Fri, 26 Jun 2020 08:03:04: #2 finished! INFO @ Fri, 26 Jun 2020 08:03:04: #2 predicted fragment length is 158 bps INFO @ Fri, 26 Jun 2020 08:03:04: #2 alternative fragment length(s) may be 4,158 bps INFO @ Fri, 26 Jun 2020 08:03:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX747302/SRX747302.20_model.r INFO @ Fri, 26 Jun 2020 08:03:04: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:03:04: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:03:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX747302/SRX747302.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:03:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX747302/SRX747302.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:03:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX747302/SRX747302.10_summits.bed INFO @ Fri, 26 Jun 2020 08:03:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4000 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:03:31: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:03:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX747302/SRX747302.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:03:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX747302/SRX747302.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:03:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX747302/SRX747302.20_summits.bed INFO @ Fri, 26 Jun 2020 08:03:45: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1079 records, 4 fields): 3 millis CompletedMACS2peakCalling