Job ID = 6497462 SRX = SRX494963 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:34:19 prefetch.2.10.7: 1) Downloading 'SRR1198495'... 2020-06-25T22:34:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:36:47 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:36:47 prefetch.2.10.7: 1) 'SRR1198495' was downloaded successfully Read 22504141 spots for SRR1198495/SRR1198495.sra Written 22504141 spots for SRR1198495/SRR1198495.sra 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: 00:04:53 22504141 reads; of these: 22504141 (100.00%) were unpaired; of these: 345310 (1.53%) aligned 0 times 18250992 (81.10%) aligned exactly 1 time 3907839 (17.36%) aligned >1 times 98.47% overall alignment rate Time searching: 00:04:53 Overall time: 00:04:53 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_sort_core] merging from 12 files... [bam_rmdupse_core] 4553608 / 22158831 = 0.2055 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 07:47:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494963/SRX494963.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494963/SRX494963.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494963/SRX494963.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494963/SRX494963.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 07:47:02: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:47:02: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:47:09: 1000000 INFO @ Fri, 26 Jun 2020 07:47:15: 2000000 INFO @ Fri, 26 Jun 2020 07:47:21: 3000000 INFO @ Fri, 26 Jun 2020 07:47:28: 4000000 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 07:47:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494963/SRX494963.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494963/SRX494963.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494963/SRX494963.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494963/SRX494963.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 07:47:33: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:47:33: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:47:34: 5000000 INFO @ Fri, 26 Jun 2020 07:47:41: 1000000 INFO @ Fri, 26 Jun 2020 07:47:43: 6000000 INFO @ Fri, 26 Jun 2020 07:47:50: 2000000 INFO @ Fri, 26 Jun 2020 07:47:52: 7000000 INFO @ Fri, 26 Jun 2020 07:47:58: 3000000 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 07:48:01: 8000000 INFO @ Fri, 26 Jun 2020 07:48:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494963/SRX494963.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494963/SRX494963.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494963/SRX494963.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494963/SRX494963.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 07:48:03: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:48:03: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:48:07: 4000000 INFO @ Fri, 26 Jun 2020 07:48:10: 9000000 INFO @ Fri, 26 Jun 2020 07:48:12: 1000000 INFO @ Fri, 26 Jun 2020 07:48:17: 5000000 INFO @ Fri, 26 Jun 2020 07:48:20: 10000000 INFO @ Fri, 26 Jun 2020 07:48:21: 2000000 INFO @ Fri, 26 Jun 2020 07:48:26: 6000000 INFO @ Fri, 26 Jun 2020 07:48:29: 11000000 INFO @ Fri, 26 Jun 2020 07:48:31: 3000000 INFO @ Fri, 26 Jun 2020 07:48:36: 7000000 INFO @ Fri, 26 Jun 2020 07:48:39: 12000000 INFO @ Fri, 26 Jun 2020 07:48:41: 4000000 INFO @ Fri, 26 Jun 2020 07:48:46: 8000000 INFO @ Fri, 26 Jun 2020 07:48:48: 13000000 INFO @ Fri, 26 Jun 2020 07:48:49: 5000000 INFO @ Fri, 26 Jun 2020 07:48:53: 9000000 INFO @ Fri, 26 Jun 2020 07:48:55: 14000000 INFO @ Fri, 26 Jun 2020 07:48:57: 6000000 INFO @ Fri, 26 Jun 2020 07:49:00: 10000000 INFO @ Fri, 26 Jun 2020 07:49:02: 15000000 INFO @ Fri, 26 Jun 2020 07:49:04: 7000000 INFO @ Fri, 26 Jun 2020 07:49:07: 11000000 INFO @ Fri, 26 Jun 2020 07:49:09: 16000000 INFO @ Fri, 26 Jun 2020 07:49:12: 8000000 INFO @ Fri, 26 Jun 2020 07:49:14: 12000000 INFO @ Fri, 26 Jun 2020 07:49:16: 17000000 INFO @ Fri, 26 Jun 2020 07:49:19: 9000000 INFO @ Fri, 26 Jun 2020 07:49:21: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:49:21: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:49:21: #1 total tags in treatment: 17605223 INFO @ Fri, 26 Jun 2020 07:49:21: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:49:21: #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 07:49:21: #1 tags after filtering in treatment: 17605223 INFO @ Fri, 26 Jun 2020 07:49:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:49:21: #1 finished! INFO @ Fri, 26 Jun 2020 07:49:21: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:49:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:49:21: 13000000 INFO @ Fri, 26 Jun 2020 07:49:22: #2 number of paired peaks: 281 WARNING @ Fri, 26 Jun 2020 07:49:22: Fewer paired peaks (281) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 281 pairs to build model! INFO @ Fri, 26 Jun 2020 07:49:22: start model_add_line... INFO @ Fri, 26 Jun 2020 07:49:22: start X-correlation... INFO @ Fri, 26 Jun 2020 07:49:22: end of X-cor INFO @ Fri, 26 Jun 2020 07:49:22: #2 finished! INFO @ Fri, 26 Jun 2020 07:49:22: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:49:22: #2 alternative fragment length(s) may be 1,37,564 bps INFO @ Fri, 26 Jun 2020 07:49:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494963/SRX494963.05_model.r WARNING @ Fri, 26 Jun 2020 07:49:22: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:49:22: #2 You may need to consider one of the other alternative d(s): 1,37,564 WARNING @ Fri, 26 Jun 2020 07:49:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:49:22: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:49:22: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:49:26: 10000000 INFO @ Fri, 26 Jun 2020 07:49:28: 14000000 INFO @ Fri, 26 Jun 2020 07:49:33: 11000000 INFO @ Fri, 26 Jun 2020 07:49:35: 15000000 INFO @ Fri, 26 Jun 2020 07:49:40: 12000000 INFO @ Fri, 26 Jun 2020 07:49:42: 16000000 INFO @ Fri, 26 Jun 2020 07:49:48: 13000000 INFO @ Fri, 26 Jun 2020 07:49:49: 17000000 INFO @ Fri, 26 Jun 2020 07:49:51: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:49:54: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:49:54: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:49:54: #1 total tags in treatment: 17605223 INFO @ Fri, 26 Jun 2020 07:49:54: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:49:54: #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 07:49:54: #1 tags after filtering in treatment: 17605223 INFO @ Fri, 26 Jun 2020 07:49:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:49:54: #1 finished! INFO @ Fri, 26 Jun 2020 07:49:54: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:49:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:49:55: 14000000 INFO @ Fri, 26 Jun 2020 07:49:55: #2 number of paired peaks: 281 WARNING @ Fri, 26 Jun 2020 07:49:55: Fewer paired peaks (281) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 281 pairs to build model! INFO @ Fri, 26 Jun 2020 07:49:55: start model_add_line... INFO @ Fri, 26 Jun 2020 07:49:55: start X-correlation... INFO @ Fri, 26 Jun 2020 07:49:55: end of X-cor INFO @ Fri, 26 Jun 2020 07:49:55: #2 finished! INFO @ Fri, 26 Jun 2020 07:49:55: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:49:55: #2 alternative fragment length(s) may be 1,37,564 bps INFO @ Fri, 26 Jun 2020 07:49:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494963/SRX494963.10_model.r WARNING @ Fri, 26 Jun 2020 07:49:55: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:49:55: #2 You may need to consider one of the other alternative d(s): 1,37,564 WARNING @ Fri, 26 Jun 2020 07:49:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:49:55: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:49:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:50:01: 15000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:50:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494963/SRX494963.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:50:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494963/SRX494963.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:50:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494963/SRX494963.05_summits.bed INFO @ Fri, 26 Jun 2020 07:50:05: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:50:07: 16000000 INFO @ Fri, 26 Jun 2020 07:50:14: 17000000 INFO @ Fri, 26 Jun 2020 07:50:17: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:50:17: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:50:17: #1 total tags in treatment: 17605223 INFO @ Fri, 26 Jun 2020 07:50:17: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:50:17: #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 07:50:18: #1 tags after filtering in treatment: 17605223 INFO @ Fri, 26 Jun 2020 07:50:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:50:18: #1 finished! INFO @ Fri, 26 Jun 2020 07:50:18: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:50:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:50:19: #2 number of paired peaks: 281 WARNING @ Fri, 26 Jun 2020 07:50:19: Fewer paired peaks (281) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 281 pairs to build model! INFO @ Fri, 26 Jun 2020 07:50:19: start model_add_line... INFO @ Fri, 26 Jun 2020 07:50:19: start X-correlation... INFO @ Fri, 26 Jun 2020 07:50:19: end of X-cor INFO @ Fri, 26 Jun 2020 07:50:19: #2 finished! INFO @ Fri, 26 Jun 2020 07:50:19: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:50:19: #2 alternative fragment length(s) may be 1,37,564 bps INFO @ Fri, 26 Jun 2020 07:50:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494963/SRX494963.20_model.r WARNING @ Fri, 26 Jun 2020 07:50:19: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:50:19: #2 You may need to consider one of the other alternative d(s): 1,37,564 WARNING @ Fri, 26 Jun 2020 07:50:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:50:19: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:50:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:50:23: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:50:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494963/SRX494963.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:50:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494963/SRX494963.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:50:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494963/SRX494963.10_summits.bed INFO @ Fri, 26 Jun 2020 07:50:37: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:50:48: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:51:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494963/SRX494963.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:51:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494963/SRX494963.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:51:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494963/SRX494963.20_summits.bed INFO @ Fri, 26 Jun 2020 07:51:01: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling