Job ID = 6497417 SRX = SRX494829 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:14:30 prefetch.2.10.7: 1) Downloading 'SRR1198361'... 2020-06-25T22:14:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:16:58 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:16:58 prefetch.2.10.7: 1) 'SRR1198361' was downloaded successfully Read 29041160 spots for SRR1198361/SRR1198361.sra Written 29041160 spots for SRR1198361/SRR1198361.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: 00:03:51 29041160 reads; of these: 29041160 (100.00%) were unpaired; of these: 10751669 (37.02%) aligned 0 times 15212122 (52.38%) aligned exactly 1 time 3077369 (10.60%) aligned >1 times 62.98% overall alignment rate Time searching: 00:03:53 Overall time: 00:03:53 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 8 files... [bam_rmdupse_core] 1906340 / 18289491 = 0.1042 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 07:26:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494829/SRX494829.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494829/SRX494829.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494829/SRX494829.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494829/SRX494829.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 07:26:55: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:26:55: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:27:02: 1000000 INFO @ Fri, 26 Jun 2020 07:27:09: 2000000 INFO @ Fri, 26 Jun 2020 07:27:15: 3000000 INFO @ Fri, 26 Jun 2020 07:27:22: 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 07:27:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494829/SRX494829.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494829/SRX494829.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494829/SRX494829.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494829/SRX494829.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 07:27:25: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:27:25: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:27:29: 5000000 INFO @ Fri, 26 Jun 2020 07:27:32: 1000000 INFO @ Fri, 26 Jun 2020 07:27:36: 6000000 INFO @ Fri, 26 Jun 2020 07:27:39: 2000000 INFO @ Fri, 26 Jun 2020 07:27:44: 7000000 INFO @ Fri, 26 Jun 2020 07:27:46: 3000000 INFO @ Fri, 26 Jun 2020 07:27:51: 8000000 INFO @ Fri, 26 Jun 2020 07:27:53: 4000000 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 07:27:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494829/SRX494829.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494829/SRX494829.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494829/SRX494829.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494829/SRX494829.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 07:27:55: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:27:55: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:27:58: 9000000 INFO @ Fri, 26 Jun 2020 07:28:00: 5000000 INFO @ Fri, 26 Jun 2020 07:28:03: 1000000 INFO @ Fri, 26 Jun 2020 07:28:05: 10000000 INFO @ Fri, 26 Jun 2020 07:28:08: 6000000 INFO @ Fri, 26 Jun 2020 07:28:11: 2000000 INFO @ Fri, 26 Jun 2020 07:28:12: 11000000 INFO @ Fri, 26 Jun 2020 07:28:15: 7000000 INFO @ Fri, 26 Jun 2020 07:28:18: 12000000 INFO @ Fri, 26 Jun 2020 07:28:19: 3000000 INFO @ Fri, 26 Jun 2020 07:28:22: 8000000 INFO @ Fri, 26 Jun 2020 07:28:25: 13000000 INFO @ Fri, 26 Jun 2020 07:28:27: 4000000 INFO @ Fri, 26 Jun 2020 07:28:29: 9000000 INFO @ Fri, 26 Jun 2020 07:28:32: 14000000 INFO @ Fri, 26 Jun 2020 07:28:35: 5000000 INFO @ Fri, 26 Jun 2020 07:28:37: 10000000 INFO @ Fri, 26 Jun 2020 07:28:39: 15000000 INFO @ Fri, 26 Jun 2020 07:28:43: 6000000 INFO @ Fri, 26 Jun 2020 07:28:44: 11000000 INFO @ Fri, 26 Jun 2020 07:28:46: 16000000 INFO @ Fri, 26 Jun 2020 07:28:48: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:28:48: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:28:48: #1 total tags in treatment: 16383151 INFO @ Fri, 26 Jun 2020 07:28:48: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:28:48: #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 07:28:49: #1 tags after filtering in treatment: 16383151 INFO @ Fri, 26 Jun 2020 07:28:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:28:49: #1 finished! INFO @ Fri, 26 Jun 2020 07:28:49: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:28:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:28:50: #2 number of paired peaks: 205 WARNING @ Fri, 26 Jun 2020 07:28:50: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Fri, 26 Jun 2020 07:28:50: start model_add_line... INFO @ Fri, 26 Jun 2020 07:28:50: start X-correlation... INFO @ Fri, 26 Jun 2020 07:28:50: end of X-cor INFO @ Fri, 26 Jun 2020 07:28:50: #2 finished! INFO @ Fri, 26 Jun 2020 07:28:50: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:28:50: #2 alternative fragment length(s) may be 1,16,35,109,422,541,565,583 bps INFO @ Fri, 26 Jun 2020 07:28:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494829/SRX494829.05_model.r WARNING @ Fri, 26 Jun 2020 07:28:50: #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 07:28:50: #2 You may need to consider one of the other alternative d(s): 1,16,35,109,422,541,565,583 WARNING @ Fri, 26 Jun 2020 07:28:50: #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 07:28:50: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:28:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:28:50: 7000000 INFO @ Fri, 26 Jun 2020 07:28:51: 12000000 INFO @ Fri, 26 Jun 2020 07:28:58: 8000000 INFO @ Fri, 26 Jun 2020 07:28:58: 13000000 INFO @ Fri, 26 Jun 2020 07:29:05: 9000000 INFO @ Fri, 26 Jun 2020 07:29:05: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:29:12: 15000000 INFO @ Fri, 26 Jun 2020 07:29:13: 10000000 INFO @ Fri, 26 Jun 2020 07:29:18: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:29:19: 16000000 INFO @ Fri, 26 Jun 2020 07:29:20: 11000000 INFO @ Fri, 26 Jun 2020 07:29:22: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:29:22: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:29:22: #1 total tags in treatment: 16383151 INFO @ Fri, 26 Jun 2020 07:29:22: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:29:22: #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 07:29:22: #1 tags after filtering in treatment: 16383151 INFO @ Fri, 26 Jun 2020 07:29:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:29:22: #1 finished! INFO @ Fri, 26 Jun 2020 07:29:22: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:29:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:29:23: #2 number of paired peaks: 205 WARNING @ Fri, 26 Jun 2020 07:29:23: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Fri, 26 Jun 2020 07:29:23: start model_add_line... INFO @ Fri, 26 Jun 2020 07:29:23: start X-correlation... INFO @ Fri, 26 Jun 2020 07:29:23: end of X-cor INFO @ Fri, 26 Jun 2020 07:29:23: #2 finished! INFO @ Fri, 26 Jun 2020 07:29:23: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:29:23: #2 alternative fragment length(s) may be 1,16,35,109,422,541,565,583 bps INFO @ Fri, 26 Jun 2020 07:29:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494829/SRX494829.10_model.r WARNING @ Fri, 26 Jun 2020 07:29:23: #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 07:29:23: #2 You may need to consider one of the other alternative d(s): 1,16,35,109,422,541,565,583 WARNING @ Fri, 26 Jun 2020 07:29:23: #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 07:29:23: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:29:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:29:27: 12000000 INFO @ Fri, 26 Jun 2020 07:29:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494829/SRX494829.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:29:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494829/SRX494829.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:29:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494829/SRX494829.05_summits.bed INFO @ Fri, 26 Jun 2020 07:29:33: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:29:34: 13000000 INFO @ Fri, 26 Jun 2020 07:29:40: 14000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:29:47: 15000000 INFO @ Fri, 26 Jun 2020 07:29:51: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:29:54: 16000000 INFO @ Fri, 26 Jun 2020 07:29:56: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:29:56: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:29:56: #1 total tags in treatment: 16383151 INFO @ Fri, 26 Jun 2020 07:29:56: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:29:56: #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 07:29:57: #1 tags after filtering in treatment: 16383151 INFO @ Fri, 26 Jun 2020 07:29:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:29:57: #1 finished! INFO @ Fri, 26 Jun 2020 07:29:57: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:29:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:29:58: #2 number of paired peaks: 205 WARNING @ Fri, 26 Jun 2020 07:29:58: Fewer paired peaks (205) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 205 pairs to build model! INFO @ Fri, 26 Jun 2020 07:29:58: start model_add_line... INFO @ Fri, 26 Jun 2020 07:29:58: start X-correlation... INFO @ Fri, 26 Jun 2020 07:29:58: end of X-cor INFO @ Fri, 26 Jun 2020 07:29:58: #2 finished! INFO @ Fri, 26 Jun 2020 07:29:58: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:29:58: #2 alternative fragment length(s) may be 1,16,35,109,422,541,565,583 bps INFO @ Fri, 26 Jun 2020 07:29:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494829/SRX494829.20_model.r WARNING @ Fri, 26 Jun 2020 07:29:58: #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 07:29:58: #2 You may need to consider one of the other alternative d(s): 1,16,35,109,422,541,565,583 WARNING @ Fri, 26 Jun 2020 07:29:58: #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 07:29:58: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:29:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:30:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494829/SRX494829.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:30:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494829/SRX494829.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:30:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494829/SRX494829.10_summits.bed INFO @ Fri, 26 Jun 2020 07:30:03: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:30:25: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:30:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494829/SRX494829.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:30:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494829/SRX494829.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:30:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494829/SRX494829.20_summits.bed INFO @ Fri, 26 Jun 2020 07:30:38: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling