Job ID = 14159351 SRX = SRX9120606 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: 00:07:14 37410483 reads; of these: 37410483 (100.00%) were unpaired; of these: 6038931 (16.14%) aligned 0 times 26041623 (69.61%) aligned exactly 1 time 5329929 (14.25%) aligned >1 times 83.86% overall alignment rate Time searching: 00:07:14 Overall time: 00:07:14 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] 6016113 / 31371552 = 0.1918 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 21:23:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.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 21:23:55: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:23:55: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:24:00: 1000000 INFO @ Wed, 08 Dec 2021 21:24:05: 2000000 INFO @ Wed, 08 Dec 2021 21:24:09: 3000000 INFO @ Wed, 08 Dec 2021 21:24:14: 4000000 INFO @ Wed, 08 Dec 2021 21:24:18: 5000000 INFO @ Wed, 08 Dec 2021 21:24:23: 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 21:24:27: 7000000 INFO @ Wed, 08 Dec 2021 21:24:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.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 21:24:30: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:24:30: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:24:32: 8000000 INFO @ Wed, 08 Dec 2021 21:24:36: 1000000 INFO @ Wed, 08 Dec 2021 21:24:37: 9000000 INFO @ Wed, 08 Dec 2021 21:24:41: 2000000 INFO @ Wed, 08 Dec 2021 21:24:42: 10000000 INFO @ Wed, 08 Dec 2021 21:24:47: 11000000 INFO @ Wed, 08 Dec 2021 21:24:47: 3000000 INFO @ Wed, 08 Dec 2021 21:24:51: 12000000 INFO @ Wed, 08 Dec 2021 21:24:52: 4000000 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 21:24:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.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 21:24:55: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:24:55: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:24:56: 13000000 INFO @ Wed, 08 Dec 2021 21:24:57: 5000000 INFO @ Wed, 08 Dec 2021 21:25:00: 1000000 INFO @ Wed, 08 Dec 2021 21:25:01: 14000000 INFO @ Wed, 08 Dec 2021 21:25:03: 6000000 INFO @ Wed, 08 Dec 2021 21:25:05: 2000000 INFO @ Wed, 08 Dec 2021 21:25:06: 15000000 INFO @ Wed, 08 Dec 2021 21:25:08: 7000000 INFO @ Wed, 08 Dec 2021 21:25:10: 3000000 INFO @ Wed, 08 Dec 2021 21:25:11: 16000000 INFO @ Wed, 08 Dec 2021 21:25:14: 8000000 INFO @ Wed, 08 Dec 2021 21:25:15: 4000000 INFO @ Wed, 08 Dec 2021 21:25:16: 17000000 INFO @ Wed, 08 Dec 2021 21:25:19: 9000000 INFO @ Wed, 08 Dec 2021 21:25:20: 5000000 INFO @ Wed, 08 Dec 2021 21:25:21: 18000000 INFO @ Wed, 08 Dec 2021 21:25:25: 10000000 INFO @ Wed, 08 Dec 2021 21:25:25: 6000000 INFO @ Wed, 08 Dec 2021 21:25:26: 19000000 INFO @ Wed, 08 Dec 2021 21:25:30: 7000000 INFO @ Wed, 08 Dec 2021 21:25:30: 11000000 INFO @ Wed, 08 Dec 2021 21:25:31: 20000000 INFO @ Wed, 08 Dec 2021 21:25:35: 8000000 INFO @ Wed, 08 Dec 2021 21:25:36: 12000000 INFO @ Wed, 08 Dec 2021 21:25:36: 21000000 INFO @ Wed, 08 Dec 2021 21:25:40: 9000000 INFO @ Wed, 08 Dec 2021 21:25:41: 22000000 INFO @ Wed, 08 Dec 2021 21:25:41: 13000000 INFO @ Wed, 08 Dec 2021 21:25:45: 10000000 INFO @ Wed, 08 Dec 2021 21:25:46: 23000000 INFO @ Wed, 08 Dec 2021 21:25:47: 14000000 INFO @ Wed, 08 Dec 2021 21:25:50: 11000000 INFO @ Wed, 08 Dec 2021 21:25:51: 24000000 INFO @ Wed, 08 Dec 2021 21:25:52: 15000000 INFO @ Wed, 08 Dec 2021 21:25:55: 12000000 INFO @ Wed, 08 Dec 2021 21:25:55: 25000000 INFO @ Wed, 08 Dec 2021 21:25:57: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 21:25:57: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 21:25:57: #1 total tags in treatment: 25355439 INFO @ Wed, 08 Dec 2021 21:25:57: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:25:57: #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 21:25:58: 16000000 INFO @ Wed, 08 Dec 2021 21:25:58: #1 tags after filtering in treatment: 25355439 INFO @ Wed, 08 Dec 2021 21:25:58: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 21:25:58: #1 finished! INFO @ Wed, 08 Dec 2021 21:25:58: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:25:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:25:59: #2 number of paired peaks: 159 WARNING @ Wed, 08 Dec 2021 21:25:59: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Wed, 08 Dec 2021 21:25:59: start model_add_line... INFO @ Wed, 08 Dec 2021 21:25:59: start X-correlation... INFO @ Wed, 08 Dec 2021 21:25:59: end of X-cor INFO @ Wed, 08 Dec 2021 21:25:59: #2 finished! INFO @ Wed, 08 Dec 2021 21:25:59: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 21:25:59: #2 alternative fragment length(s) may be 1,36,41,112,594 bps INFO @ Wed, 08 Dec 2021 21:25:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.05_model.r WARNING @ Wed, 08 Dec 2021 21:25:59: #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 21:25:59: #2 You may need to consider one of the other alternative d(s): 1,36,41,112,594 WARNING @ Wed, 08 Dec 2021 21:25:59: #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 21:25:59: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:25:59: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:26:00: 13000000 INFO @ Wed, 08 Dec 2021 21:26:03: 17000000 INFO @ Wed, 08 Dec 2021 21:26:05: 14000000 INFO @ Wed, 08 Dec 2021 21:26:08: 18000000 INFO @ Wed, 08 Dec 2021 21:26:09: 15000000 INFO @ Wed, 08 Dec 2021 21:26:14: 19000000 INFO @ Wed, 08 Dec 2021 21:26:14: 16000000 INFO @ Wed, 08 Dec 2021 21:26:19: 20000000 INFO @ Wed, 08 Dec 2021 21:26:19: 17000000 INFO @ Wed, 08 Dec 2021 21:26:24: 18000000 INFO @ Wed, 08 Dec 2021 21:26:25: 21000000 INFO @ Wed, 08 Dec 2021 21:26:29: 19000000 INFO @ Wed, 08 Dec 2021 21:26:30: 22000000 INFO @ Wed, 08 Dec 2021 21:26:34: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 21:26:36: 23000000 INFO @ Wed, 08 Dec 2021 21:26:36: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:26:39: 21000000 INFO @ Wed, 08 Dec 2021 21:26:41: 24000000 INFO @ Wed, 08 Dec 2021 21:26:44: 22000000 INFO @ Wed, 08 Dec 2021 21:26:46: 25000000 INFO @ Wed, 08 Dec 2021 21:26:48: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 21:26:48: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 21:26:48: #1 total tags in treatment: 25355439 INFO @ Wed, 08 Dec 2021 21:26:48: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:26:48: #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 21:26:49: #1 tags after filtering in treatment: 25355439 INFO @ Wed, 08 Dec 2021 21:26:49: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 21:26:49: #1 finished! INFO @ Wed, 08 Dec 2021 21:26:49: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:26:49: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:26:49: 23000000 INFO @ Wed, 08 Dec 2021 21:26:50: #2 number of paired peaks: 159 WARNING @ Wed, 08 Dec 2021 21:26:50: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Wed, 08 Dec 2021 21:26:50: start model_add_line... INFO @ Wed, 08 Dec 2021 21:26:50: start X-correlation... INFO @ Wed, 08 Dec 2021 21:26:51: end of X-cor INFO @ Wed, 08 Dec 2021 21:26:51: #2 finished! INFO @ Wed, 08 Dec 2021 21:26:51: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 21:26:51: #2 alternative fragment length(s) may be 1,36,41,112,594 bps INFO @ Wed, 08 Dec 2021 21:26:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.10_model.r WARNING @ Wed, 08 Dec 2021 21:26:51: #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 21:26:51: #2 You may need to consider one of the other alternative d(s): 1,36,41,112,594 WARNING @ Wed, 08 Dec 2021 21:26:51: #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 21:26:51: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:26:51: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:26:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.05_peaks.xls INFO @ Wed, 08 Dec 2021 21:26:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:26:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.05_summits.bed INFO @ Wed, 08 Dec 2021 21:26:52: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:26:54: 24000000 INFO @ Wed, 08 Dec 2021 21:26:59: 25000000 INFO @ Wed, 08 Dec 2021 21:27:00: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 21:27:00: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 21:27:00: #1 total tags in treatment: 25355439 INFO @ Wed, 08 Dec 2021 21:27:00: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:27:00: #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 21:27:01: #1 tags after filtering in treatment: 25355439 INFO @ Wed, 08 Dec 2021 21:27:01: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 21:27:01: #1 finished! INFO @ Wed, 08 Dec 2021 21:27:01: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:27:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:27:02: #2 number of paired peaks: 159 WARNING @ Wed, 08 Dec 2021 21:27:02: Fewer paired peaks (159) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 159 pairs to build model! INFO @ Wed, 08 Dec 2021 21:27:02: start model_add_line... INFO @ Wed, 08 Dec 2021 21:27:02: start X-correlation... INFO @ Wed, 08 Dec 2021 21:27:02: end of X-cor INFO @ Wed, 08 Dec 2021 21:27:02: #2 finished! INFO @ Wed, 08 Dec 2021 21:27:02: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 21:27:02: #2 alternative fragment length(s) may be 1,36,41,112,594 bps INFO @ Wed, 08 Dec 2021 21:27:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.20_model.r WARNING @ Wed, 08 Dec 2021 21:27:02: #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 21:27:02: #2 You may need to consider one of the other alternative d(s): 1,36,41,112,594 WARNING @ Wed, 08 Dec 2021 21:27:02: #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 21:27:02: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:27:02: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:27:27: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 21:27:37: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:27:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.10_peaks.xls INFO @ Wed, 08 Dec 2021 21:27:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:27:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.10_summits.bed INFO @ Wed, 08 Dec 2021 21:27:43: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:27:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.20_peaks.xls INFO @ Wed, 08 Dec 2021 21:27:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:27:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120606/SRX9120606.20_summits.bed INFO @ Wed, 08 Dec 2021 21:27:53: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling