Job ID = 10165955 SRX = SRX8331147 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: 00:11:01 30081170 reads; of these: 30081170 (100.00%) were unpaired; of these: 684508 (2.28%) aligned 0 times 24947507 (82.93%) aligned exactly 1 time 4449155 (14.79%) aligned >1 times 97.72% overall alignment rate Time searching: 00:11:01 Overall time: 00:11:01 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] 7603621 / 29396662 = 0.2587 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 @ Thu, 08 Oct 2020 20:36:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8331147/SRX8331147.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8331147/SRX8331147.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8331147/SRX8331147.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8331147/SRX8331147.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 @ Thu, 08 Oct 2020 20:36:54: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:36:54: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:36:59: 1000000 INFO @ Thu, 08 Oct 2020 20:37:05: 2000000 INFO @ Thu, 08 Oct 2020 20:37:11: 3000000 INFO @ Thu, 08 Oct 2020 20:37:16: 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 @ Thu, 08 Oct 2020 20:37:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8331147/SRX8331147.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8331147/SRX8331147.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8331147/SRX8331147.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8331147/SRX8331147.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 @ Thu, 08 Oct 2020 20:37:22: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:37:22: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:37:22: 5000000 INFO @ Thu, 08 Oct 2020 20:37:28: 1000000 INFO @ Thu, 08 Oct 2020 20:37:28: 6000000 INFO @ Thu, 08 Oct 2020 20:37:34: 2000000 INFO @ Thu, 08 Oct 2020 20:37:35: 7000000 INFO @ Thu, 08 Oct 2020 20:37:41: 3000000 INFO @ Thu, 08 Oct 2020 20:37:41: 8000000 INFO @ Thu, 08 Oct 2020 20:37:47: 4000000 INFO @ Thu, 08 Oct 2020 20:37:47: 9000000 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 @ Thu, 08 Oct 2020 20:37:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8331147/SRX8331147.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8331147/SRX8331147.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8331147/SRX8331147.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8331147/SRX8331147.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 @ Thu, 08 Oct 2020 20:37:52: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:37:52: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:37:53: 10000000 INFO @ Thu, 08 Oct 2020 20:37:53: 5000000 INFO @ Thu, 08 Oct 2020 20:37:58: 1000000 INFO @ Thu, 08 Oct 2020 20:37:59: 11000000 INFO @ Thu, 08 Oct 2020 20:38:00: 6000000 INFO @ Thu, 08 Oct 2020 20:38:05: 2000000 INFO @ Thu, 08 Oct 2020 20:38:06: 12000000 INFO @ Thu, 08 Oct 2020 20:38:06: 7000000 INFO @ Thu, 08 Oct 2020 20:38:11: 3000000 INFO @ Thu, 08 Oct 2020 20:38:12: 13000000 INFO @ Thu, 08 Oct 2020 20:38:13: 8000000 INFO @ Thu, 08 Oct 2020 20:38:17: 4000000 INFO @ Thu, 08 Oct 2020 20:38:18: 14000000 INFO @ Thu, 08 Oct 2020 20:38:19: 9000000 INFO @ Thu, 08 Oct 2020 20:38:24: 5000000 INFO @ Thu, 08 Oct 2020 20:38:25: 15000000 INFO @ Thu, 08 Oct 2020 20:38:25: 10000000 INFO @ Thu, 08 Oct 2020 20:38:30: 6000000 INFO @ Thu, 08 Oct 2020 20:38:31: 16000000 INFO @ Thu, 08 Oct 2020 20:38:31: 11000000 INFO @ Thu, 08 Oct 2020 20:38:36: 7000000 INFO @ Thu, 08 Oct 2020 20:38:37: 17000000 INFO @ Thu, 08 Oct 2020 20:38:38: 12000000 INFO @ Thu, 08 Oct 2020 20:38:43: 8000000 INFO @ Thu, 08 Oct 2020 20:38:43: 18000000 INFO @ Thu, 08 Oct 2020 20:38:44: 13000000 INFO @ Thu, 08 Oct 2020 20:38:49: 9000000 INFO @ Thu, 08 Oct 2020 20:38:49: 19000000 INFO @ Thu, 08 Oct 2020 20:38:50: 14000000 INFO @ Thu, 08 Oct 2020 20:38:55: 10000000 INFO @ Thu, 08 Oct 2020 20:38:55: 20000000 INFO @ Thu, 08 Oct 2020 20:38:56: 15000000 INFO @ Thu, 08 Oct 2020 20:39:01: 11000000 INFO @ Thu, 08 Oct 2020 20:39:02: 21000000 INFO @ Thu, 08 Oct 2020 20:39:03: 16000000 INFO @ Thu, 08 Oct 2020 20:39:07: #1 tag size is determined as 68 bps INFO @ Thu, 08 Oct 2020 20:39:07: #1 tag size = 68 INFO @ Thu, 08 Oct 2020 20:39:07: #1 total tags in treatment: 21793041 INFO @ Thu, 08 Oct 2020 20:39:07: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:39:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:39:07: #1 tags after filtering in treatment: 21793041 INFO @ Thu, 08 Oct 2020 20:39:07: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:39:07: #1 finished! INFO @ Thu, 08 Oct 2020 20:39:07: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:39:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:39:07: 12000000 INFO @ Thu, 08 Oct 2020 20:39:08: #2 number of paired peaks: 149 WARNING @ Thu, 08 Oct 2020 20:39:08: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Thu, 08 Oct 2020 20:39:08: start model_add_line... INFO @ Thu, 08 Oct 2020 20:39:08: start X-correlation... INFO @ Thu, 08 Oct 2020 20:39:08: end of X-cor INFO @ Thu, 08 Oct 2020 20:39:08: #2 finished! INFO @ Thu, 08 Oct 2020 20:39:08: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:39:08: #2 alternative fragment length(s) may be 1,12,15,468,539,568 bps INFO @ Thu, 08 Oct 2020 20:39:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8331147/SRX8331147.05_model.r WARNING @ Thu, 08 Oct 2020 20:39:08: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:39:08: #2 You may need to consider one of the other alternative d(s): 1,12,15,468,539,568 WARNING @ Thu, 08 Oct 2020 20:39:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:39:08: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:39:08: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:39:09: 17000000 INFO @ Thu, 08 Oct 2020 20:39:14: 13000000 INFO @ Thu, 08 Oct 2020 20:39:15: 18000000 INFO @ Thu, 08 Oct 2020 20:39:20: 14000000 INFO @ Thu, 08 Oct 2020 20:39:21: 19000000 INFO @ Thu, 08 Oct 2020 20:39:26: 15000000 INFO @ Thu, 08 Oct 2020 20:39:27: 20000000 INFO @ Thu, 08 Oct 2020 20:39:32: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:39:33: 21000000 INFO @ Thu, 08 Oct 2020 20:39:38: 17000000 INFO @ Thu, 08 Oct 2020 20:39:38: #1 tag size is determined as 68 bps INFO @ Thu, 08 Oct 2020 20:39:38: #1 tag size = 68 INFO @ Thu, 08 Oct 2020 20:39:38: #1 total tags in treatment: 21793041 INFO @ Thu, 08 Oct 2020 20:39:38: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:39:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:39:39: #1 tags after filtering in treatment: 21793041 INFO @ Thu, 08 Oct 2020 20:39:39: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:39:39: #1 finished! INFO @ Thu, 08 Oct 2020 20:39:39: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:39:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:39:40: #2 number of paired peaks: 149 WARNING @ Thu, 08 Oct 2020 20:39:40: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Thu, 08 Oct 2020 20:39:40: start model_add_line... INFO @ Thu, 08 Oct 2020 20:39:40: start X-correlation... INFO @ Thu, 08 Oct 2020 20:39:40: end of X-cor INFO @ Thu, 08 Oct 2020 20:39:40: #2 finished! INFO @ Thu, 08 Oct 2020 20:39:40: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:39:40: #2 alternative fragment length(s) may be 1,12,15,468,539,568 bps INFO @ Thu, 08 Oct 2020 20:39:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8331147/SRX8331147.10_model.r WARNING @ Thu, 08 Oct 2020 20:39:40: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:39:40: #2 You may need to consider one of the other alternative d(s): 1,12,15,468,539,568 WARNING @ Thu, 08 Oct 2020 20:39:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:39:40: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:39:40: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:39:41: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:39:44: 18000000 INFO @ Thu, 08 Oct 2020 20:39:50: 19000000 INFO @ Thu, 08 Oct 2020 20:39:56: 20000000 INFO @ Thu, 08 Oct 2020 20:39:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8331147/SRX8331147.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:39:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8331147/SRX8331147.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:39:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8331147/SRX8331147.05_summits.bed INFO @ Thu, 08 Oct 2020 20:39:57: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:40:01: 21000000 INFO @ Thu, 08 Oct 2020 20:40:06: #1 tag size is determined as 68 bps INFO @ Thu, 08 Oct 2020 20:40:06: #1 tag size = 68 INFO @ Thu, 08 Oct 2020 20:40:06: #1 total tags in treatment: 21793041 INFO @ Thu, 08 Oct 2020 20:40:06: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:40:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:40:06: #1 tags after filtering in treatment: 21793041 INFO @ Thu, 08 Oct 2020 20:40:06: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:40:06: #1 finished! INFO @ Thu, 08 Oct 2020 20:40:06: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:40:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:40:08: #2 number of paired peaks: 149 WARNING @ Thu, 08 Oct 2020 20:40:08: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Thu, 08 Oct 2020 20:40:08: start model_add_line... INFO @ Thu, 08 Oct 2020 20:40:08: start X-correlation... INFO @ Thu, 08 Oct 2020 20:40:08: end of X-cor INFO @ Thu, 08 Oct 2020 20:40:08: #2 finished! INFO @ Thu, 08 Oct 2020 20:40:08: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:40:08: #2 alternative fragment length(s) may be 1,12,15,468,539,568 bps INFO @ Thu, 08 Oct 2020 20:40:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8331147/SRX8331147.20_model.r WARNING @ Thu, 08 Oct 2020 20:40:08: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:40:08: #2 You may need to consider one of the other alternative d(s): 1,12,15,468,539,568 WARNING @ Thu, 08 Oct 2020 20:40:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:40:08: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:40:08: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:40:14: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:40:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8331147/SRX8331147.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:40:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8331147/SRX8331147.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:40:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8331147/SRX8331147.10_summits.bed INFO @ Thu, 08 Oct 2020 20:40:30: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:40:42: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:40:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8331147/SRX8331147.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:40:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8331147/SRX8331147.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:40:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8331147/SRX8331147.20_summits.bed INFO @ Thu, 08 Oct 2020 20:40:58: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling