Job ID = 14159370 SRX = SRX9120607 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:07:18 41837722 reads; of these: 41837722 (100.00%) were unpaired; of these: 11196918 (26.76%) aligned 0 times 25172664 (60.17%) aligned exactly 1 time 5468140 (13.07%) aligned >1 times 73.24% overall alignment rate Time searching: 00:07:18 Overall time: 00:07:18 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 16 files... [bam_rmdupse_core] 5983297 / 30640804 = 0.1953 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 21:28:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.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 @ Wed, 08 Dec 2021 21:28:36: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:28:36: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:28:41: 1000000 INFO @ Wed, 08 Dec 2021 21:28:45: 2000000 INFO @ Wed, 08 Dec 2021 21:28:50: 3000000 INFO @ Wed, 08 Dec 2021 21:28:55: 4000000 INFO @ Wed, 08 Dec 2021 21:28:59: 5000000 INFO @ Wed, 08 Dec 2021 21:29:04: 6000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 21:29:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.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 @ Wed, 08 Dec 2021 21:29:06: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:29:06: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:29:09: 7000000 INFO @ Wed, 08 Dec 2021 21:29:11: 1000000 INFO @ Wed, 08 Dec 2021 21:29:14: 8000000 INFO @ Wed, 08 Dec 2021 21:29:16: 2000000 INFO @ Wed, 08 Dec 2021 21:29:19: 9000000 INFO @ Wed, 08 Dec 2021 21:29:21: 3000000 INFO @ Wed, 08 Dec 2021 21:29:24: 10000000 INFO @ Wed, 08 Dec 2021 21:29:26: 4000000 INFO @ Wed, 08 Dec 2021 21:29:29: 11000000 INFO @ Wed, 08 Dec 2021 21:29:31: 5000000 INFO @ Wed, 08 Dec 2021 21:29:34: 12000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 21:29:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.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 @ Wed, 08 Dec 2021 21:29:36: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:29:36: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:29:36: 6000000 INFO @ Wed, 08 Dec 2021 21:29:39: 13000000 INFO @ Wed, 08 Dec 2021 21:29:41: 7000000 INFO @ Wed, 08 Dec 2021 21:29:41: 1000000 INFO @ Wed, 08 Dec 2021 21:29:44: 14000000 INFO @ Wed, 08 Dec 2021 21:29:46: 8000000 INFO @ Wed, 08 Dec 2021 21:29:46: 2000000 INFO @ Wed, 08 Dec 2021 21:29:48: 15000000 INFO @ Wed, 08 Dec 2021 21:29:51: 9000000 INFO @ Wed, 08 Dec 2021 21:29:51: 3000000 INFO @ Wed, 08 Dec 2021 21:29:53: 16000000 INFO @ Wed, 08 Dec 2021 21:29:56: 10000000 INFO @ Wed, 08 Dec 2021 21:29:56: 4000000 INFO @ Wed, 08 Dec 2021 21:29:58: 17000000 INFO @ Wed, 08 Dec 2021 21:30:01: 11000000 INFO @ Wed, 08 Dec 2021 21:30:01: 5000000 INFO @ Wed, 08 Dec 2021 21:30:03: 18000000 INFO @ Wed, 08 Dec 2021 21:30:06: 12000000 INFO @ Wed, 08 Dec 2021 21:30:06: 6000000 INFO @ Wed, 08 Dec 2021 21:30:08: 19000000 INFO @ Wed, 08 Dec 2021 21:30:11: 13000000 INFO @ Wed, 08 Dec 2021 21:30:11: 7000000 INFO @ Wed, 08 Dec 2021 21:30:14: 20000000 INFO @ Wed, 08 Dec 2021 21:30:16: 14000000 INFO @ Wed, 08 Dec 2021 21:30:16: 8000000 INFO @ Wed, 08 Dec 2021 21:30:19: 21000000 INFO @ Wed, 08 Dec 2021 21:30:21: 15000000 INFO @ Wed, 08 Dec 2021 21:30:21: 9000000 INFO @ Wed, 08 Dec 2021 21:30:24: 22000000 INFO @ Wed, 08 Dec 2021 21:30:26: 16000000 INFO @ Wed, 08 Dec 2021 21:30:26: 10000000 INFO @ Wed, 08 Dec 2021 21:30:29: 23000000 INFO @ Wed, 08 Dec 2021 21:30:31: 17000000 INFO @ Wed, 08 Dec 2021 21:30:31: 11000000 INFO @ Wed, 08 Dec 2021 21:30:34: 24000000 INFO @ Wed, 08 Dec 2021 21:30:36: 18000000 INFO @ Wed, 08 Dec 2021 21:30:36: 12000000 INFO @ Wed, 08 Dec 2021 21:30:37: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 21:30:37: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 21:30:37: #1 total tags in treatment: 24657507 INFO @ Wed, 08 Dec 2021 21:30:37: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:30:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 21:30:38: #1 tags after filtering in treatment: 24657507 INFO @ Wed, 08 Dec 2021 21:30:38: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 21:30:38: #1 finished! INFO @ Wed, 08 Dec 2021 21:30:38: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:30:38: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:30:39: #2 number of paired peaks: 173 WARNING @ Wed, 08 Dec 2021 21:30:39: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Wed, 08 Dec 2021 21:30:39: start model_add_line... INFO @ Wed, 08 Dec 2021 21:30:39: start X-correlation... INFO @ Wed, 08 Dec 2021 21:30:39: end of X-cor INFO @ Wed, 08 Dec 2021 21:30:39: #2 finished! INFO @ Wed, 08 Dec 2021 21:30:39: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 21:30:39: #2 alternative fragment length(s) may be 1,49,550,596 bps INFO @ Wed, 08 Dec 2021 21:30:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.05_model.r WARNING @ Wed, 08 Dec 2021 21:30:39: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 21:30:39: #2 You may need to consider one of the other alternative d(s): 1,49,550,596 WARNING @ Wed, 08 Dec 2021 21:30:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 21:30:39: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:30:39: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:30:41: 19000000 INFO @ Wed, 08 Dec 2021 21:30:41: 13000000 INFO @ Wed, 08 Dec 2021 21:30:46: 20000000 INFO @ Wed, 08 Dec 2021 21:30:46: 14000000 INFO @ Wed, 08 Dec 2021 21:30:51: 21000000 INFO @ Wed, 08 Dec 2021 21:30:51: 15000000 INFO @ Wed, 08 Dec 2021 21:30:56: 22000000 INFO @ Wed, 08 Dec 2021 21:30:57: 16000000 INFO @ Wed, 08 Dec 2021 21:31:02: 17000000 INFO @ Wed, 08 Dec 2021 21:31:02: 23000000 INFO @ Wed, 08 Dec 2021 21:31:07: 18000000 INFO @ Wed, 08 Dec 2021 21:31:07: 24000000 INFO @ Wed, 08 Dec 2021 21:31:11: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 21:31:11: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 21:31:11: #1 total tags in treatment: 24657507 INFO @ Wed, 08 Dec 2021 21:31:11: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:31:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 21:31:11: #1 tags after filtering in treatment: 24657507 INFO @ Wed, 08 Dec 2021 21:31:11: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 21:31:11: #1 finished! INFO @ Wed, 08 Dec 2021 21:31:11: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:31:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:31:12: 19000000 INFO @ Wed, 08 Dec 2021 21:31:13: #2 number of paired peaks: 173 WARNING @ Wed, 08 Dec 2021 21:31:13: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Wed, 08 Dec 2021 21:31:13: start model_add_line... INFO @ Wed, 08 Dec 2021 21:31:13: start X-correlation... INFO @ Wed, 08 Dec 2021 21:31:13: end of X-cor INFO @ Wed, 08 Dec 2021 21:31:13: #2 finished! INFO @ Wed, 08 Dec 2021 21:31:13: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 21:31:13: #2 alternative fragment length(s) may be 1,49,550,596 bps INFO @ Wed, 08 Dec 2021 21:31:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.10_model.r WARNING @ Wed, 08 Dec 2021 21:31:13: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 21:31:13: #2 You may need to consider one of the other alternative d(s): 1,49,550,596 WARNING @ Wed, 08 Dec 2021 21:31:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 21:31:13: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:31:13: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:31:15: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:31:17: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 21:31:22: 21000000 INFO @ Wed, 08 Dec 2021 21:31:27: 22000000 INFO @ Wed, 08 Dec 2021 21:31:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.05_peaks.xls INFO @ Wed, 08 Dec 2021 21:31:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:31:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.05_summits.bed INFO @ Wed, 08 Dec 2021 21:31:30: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:31:32: 23000000 INFO @ Wed, 08 Dec 2021 21:31:37: 24000000 INFO @ Wed, 08 Dec 2021 21:31:40: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 21:31:40: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 21:31:40: #1 total tags in treatment: 24657507 INFO @ Wed, 08 Dec 2021 21:31:40: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:31:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 21:31:41: #1 tags after filtering in treatment: 24657507 INFO @ Wed, 08 Dec 2021 21:31:41: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 21:31:41: #1 finished! INFO @ Wed, 08 Dec 2021 21:31:41: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:31:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:31:42: #2 number of paired peaks: 173 WARNING @ Wed, 08 Dec 2021 21:31:42: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Wed, 08 Dec 2021 21:31:42: start model_add_line... INFO @ Wed, 08 Dec 2021 21:31:42: start X-correlation... INFO @ Wed, 08 Dec 2021 21:31:42: end of X-cor INFO @ Wed, 08 Dec 2021 21:31:42: #2 finished! INFO @ Wed, 08 Dec 2021 21:31:42: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 21:31:42: #2 alternative fragment length(s) may be 1,49,550,596 bps INFO @ Wed, 08 Dec 2021 21:31:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.20_model.r WARNING @ Wed, 08 Dec 2021 21:31:42: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 21:31:42: #2 You may need to consider one of the other alternative d(s): 1,49,550,596 WARNING @ Wed, 08 Dec 2021 21:31:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 21:31:42: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:31:42: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:31:47: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:32:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.10_peaks.xls INFO @ Wed, 08 Dec 2021 21:32:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:32:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.10_summits.bed INFO @ Wed, 08 Dec 2021 21:32:03: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 21:32:18: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:32:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.20_peaks.xls INFO @ Wed, 08 Dec 2021 21:32:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:32:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120607/SRX9120607.20_summits.bed INFO @ Wed, 08 Dec 2021 21:32:33: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling