Job ID = 6366569 SRX = SRX1949398 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:50:11 prefetch.2.10.7: 1) Downloading 'SRR3922838'... 2020-06-15T22:50:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:52:01 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:52:02 prefetch.2.10.7: 'SRR3922838' is valid 2020-06-15T22:52:02 prefetch.2.10.7: 1) 'SRR3922838' was downloaded successfully Read 20859731 spots for SRR3922838/SRR3922838.sra Written 20859731 spots for SRR3922838/SRR3922838.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: 00:05:03 20859731 reads; of these: 20859731 (100.00%) were unpaired; of these: 208395 (1.00%) aligned 0 times 17280617 (82.84%) aligned exactly 1 time 3370719 (16.16%) aligned >1 times 99.00% overall alignment rate Time searching: 00:05:03 Overall time: 00:05:03 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] 2035587 / 20651336 = 0.0986 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 @ Tue, 16 Jun 2020 08:04:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1949398/SRX1949398.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1949398/SRX1949398.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1949398/SRX1949398.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1949398/SRX1949398.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 @ Tue, 16 Jun 2020 08:04:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:04:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:04:09: 1000000 INFO @ Tue, 16 Jun 2020 08:04:14: 2000000 INFO @ Tue, 16 Jun 2020 08:04:20: 3000000 INFO @ Tue, 16 Jun 2020 08:04:25: 4000000 INFO @ Tue, 16 Jun 2020 08:04:31: 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 @ Tue, 16 Jun 2020 08:04:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1949398/SRX1949398.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1949398/SRX1949398.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1949398/SRX1949398.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1949398/SRX1949398.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 @ Tue, 16 Jun 2020 08:04:36: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:04:36: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:04:36: 6000000 INFO @ Tue, 16 Jun 2020 08:04:42: 1000000 INFO @ Tue, 16 Jun 2020 08:04:42: 7000000 INFO @ Tue, 16 Jun 2020 08:04:48: 2000000 INFO @ Tue, 16 Jun 2020 08:04:48: 8000000 INFO @ Tue, 16 Jun 2020 08:04:54: 3000000 INFO @ Tue, 16 Jun 2020 08:04:54: 9000000 INFO @ Tue, 16 Jun 2020 08:05:00: 10000000 INFO @ Tue, 16 Jun 2020 08:05:00: 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 @ Tue, 16 Jun 2020 08:05:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1949398/SRX1949398.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1949398/SRX1949398.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1949398/SRX1949398.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1949398/SRX1949398.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 @ Tue, 16 Jun 2020 08:05:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:05:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:05:06: 11000000 INFO @ Tue, 16 Jun 2020 08:05:06: 5000000 INFO @ Tue, 16 Jun 2020 08:05:10: 1000000 INFO @ Tue, 16 Jun 2020 08:05:12: 12000000 INFO @ Tue, 16 Jun 2020 08:05:13: 6000000 INFO @ Tue, 16 Jun 2020 08:05:16: 2000000 INFO @ Tue, 16 Jun 2020 08:05:18: 13000000 INFO @ Tue, 16 Jun 2020 08:05:19: 7000000 INFO @ Tue, 16 Jun 2020 08:05:22: 3000000 INFO @ Tue, 16 Jun 2020 08:05:24: 14000000 INFO @ Tue, 16 Jun 2020 08:05:25: 8000000 INFO @ Tue, 16 Jun 2020 08:05:29: 4000000 INFO @ Tue, 16 Jun 2020 08:05:31: 15000000 INFO @ Tue, 16 Jun 2020 08:05:31: 9000000 INFO @ Tue, 16 Jun 2020 08:05:35: 5000000 INFO @ Tue, 16 Jun 2020 08:05:37: 16000000 INFO @ Tue, 16 Jun 2020 08:05:38: 10000000 INFO @ Tue, 16 Jun 2020 08:05:41: 6000000 INFO @ Tue, 16 Jun 2020 08:05:43: 17000000 INFO @ Tue, 16 Jun 2020 08:05:44: 11000000 INFO @ Tue, 16 Jun 2020 08:05:47: 7000000 INFO @ Tue, 16 Jun 2020 08:05:49: 18000000 INFO @ Tue, 16 Jun 2020 08:05:50: 12000000 INFO @ Tue, 16 Jun 2020 08:05:52: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 08:05:52: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 08:05:52: #1 total tags in treatment: 18615749 INFO @ Tue, 16 Jun 2020 08:05:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:05:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:05:53: #1 tags after filtering in treatment: 18615749 INFO @ Tue, 16 Jun 2020 08:05:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:05:53: #1 finished! INFO @ Tue, 16 Jun 2020 08:05:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:05:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:05:53: 8000000 INFO @ Tue, 16 Jun 2020 08:05:54: #2 number of paired peaks: 212 WARNING @ Tue, 16 Jun 2020 08:05:54: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Tue, 16 Jun 2020 08:05:54: start model_add_line... INFO @ Tue, 16 Jun 2020 08:05:54: start X-correlation... INFO @ Tue, 16 Jun 2020 08:05:54: end of X-cor INFO @ Tue, 16 Jun 2020 08:05:54: #2 finished! INFO @ Tue, 16 Jun 2020 08:05:54: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:05:54: #2 alternative fragment length(s) may be 1,44,530,568 bps INFO @ Tue, 16 Jun 2020 08:05:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1949398/SRX1949398.05_model.r WARNING @ Tue, 16 Jun 2020 08:05:54: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:05:54: #2 You may need to consider one of the other alternative d(s): 1,44,530,568 WARNING @ Tue, 16 Jun 2020 08:05:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:05:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:05:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:05:56: 13000000 INFO @ Tue, 16 Jun 2020 08:05:59: 9000000 INFO @ Tue, 16 Jun 2020 08:06:02: 14000000 INFO @ Tue, 16 Jun 2020 08:06:05: 10000000 INFO @ Tue, 16 Jun 2020 08:06:08: 15000000 INFO @ Tue, 16 Jun 2020 08:06:12: 11000000 INFO @ Tue, 16 Jun 2020 08:06:14: 16000000 INFO @ Tue, 16 Jun 2020 08:06:18: 12000000 INFO @ Tue, 16 Jun 2020 08:06:20: 17000000 INFO @ Tue, 16 Jun 2020 08:06:24: 13000000 INFO @ Tue, 16 Jun 2020 08:06:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:06:26: 18000000 INFO @ Tue, 16 Jun 2020 08:06:30: 14000000 INFO @ Tue, 16 Jun 2020 08:06:30: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 08:06:30: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 08:06:30: #1 total tags in treatment: 18615749 INFO @ Tue, 16 Jun 2020 08:06:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:06:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:06:30: #1 tags after filtering in treatment: 18615749 INFO @ Tue, 16 Jun 2020 08:06:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:06:30: #1 finished! INFO @ Tue, 16 Jun 2020 08:06:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:06:30: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:06:32: #2 number of paired peaks: 212 WARNING @ Tue, 16 Jun 2020 08:06:32: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Tue, 16 Jun 2020 08:06:32: start model_add_line... INFO @ Tue, 16 Jun 2020 08:06:32: start X-correlation... INFO @ Tue, 16 Jun 2020 08:06:32: end of X-cor INFO @ Tue, 16 Jun 2020 08:06:32: #2 finished! INFO @ Tue, 16 Jun 2020 08:06:32: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:06:32: #2 alternative fragment length(s) may be 1,44,530,568 bps INFO @ Tue, 16 Jun 2020 08:06:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1949398/SRX1949398.10_model.r WARNING @ Tue, 16 Jun 2020 08:06:32: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:06:32: #2 You may need to consider one of the other alternative d(s): 1,44,530,568 WARNING @ Tue, 16 Jun 2020 08:06:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:06:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:06:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:06:35: 15000000 INFO @ Tue, 16 Jun 2020 08:06:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1949398/SRX1949398.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:06:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1949398/SRX1949398.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:06:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1949398/SRX1949398.05_summits.bed INFO @ Tue, 16 Jun 2020 08:06:40: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:06:41: 16000000 INFO @ Tue, 16 Jun 2020 08:06:47: 17000000 INFO @ Tue, 16 Jun 2020 08:06:53: 18000000 INFO @ Tue, 16 Jun 2020 08:06:56: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 08:06:56: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 08:06:56: #1 total tags in treatment: 18615749 INFO @ Tue, 16 Jun 2020 08:06:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:06:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:06:57: #1 tags after filtering in treatment: 18615749 INFO @ Tue, 16 Jun 2020 08:06:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:06:57: #1 finished! INFO @ Tue, 16 Jun 2020 08:06:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:06:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:06:58: #2 number of paired peaks: 212 WARNING @ Tue, 16 Jun 2020 08:06:58: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Tue, 16 Jun 2020 08:06:58: start model_add_line... INFO @ Tue, 16 Jun 2020 08:06:58: start X-correlation... INFO @ Tue, 16 Jun 2020 08:06:58: end of X-cor INFO @ Tue, 16 Jun 2020 08:06:58: #2 finished! INFO @ Tue, 16 Jun 2020 08:06:58: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:06:58: #2 alternative fragment length(s) may be 1,44,530,568 bps INFO @ Tue, 16 Jun 2020 08:06:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1949398/SRX1949398.20_model.r WARNING @ Tue, 16 Jun 2020 08:06:58: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:06:58: #2 You may need to consider one of the other alternative d(s): 1,44,530,568 WARNING @ Tue, 16 Jun 2020 08:06:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:06:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:06:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:07:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:07:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1949398/SRX1949398.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:07:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1949398/SRX1949398.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:07:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1949398/SRX1949398.10_summits.bed INFO @ Tue, 16 Jun 2020 08:07:18: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:07:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:07:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1949398/SRX1949398.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:07:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1949398/SRX1949398.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:07:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1949398/SRX1949398.20_summits.bed INFO @ Tue, 16 Jun 2020 08:07:44: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling