Job ID = 14159443 SRX = SRX9120620 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: 00:00:02 Multiseed full-index search: 00:06:31 23786791 reads; of these: 23786791 (100.00%) were unpaired; of these: 114568 (0.48%) aligned 0 times 19854394 (83.47%) aligned exactly 1 time 3817829 (16.05%) aligned >1 times 99.52% overall alignment rate Time searching: 00:06:33 Overall time: 00:06:33 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] 3688368 / 23672223 = 0.1558 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 22:07:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120620/SRX9120620.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120620/SRX9120620.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120620/SRX9120620.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120620/SRX9120620.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 22:07:48: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:07:48: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:07:56: 1000000 INFO @ Wed, 08 Dec 2021 22:08:03: 2000000 INFO @ Wed, 08 Dec 2021 22:08:11: 3000000 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 22:08:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120620/SRX9120620.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120620/SRX9120620.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120620/SRX9120620.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120620/SRX9120620.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 22:08:18: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:08:18: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:08:19: 4000000 INFO @ Wed, 08 Dec 2021 22:08:26: 1000000 INFO @ Wed, 08 Dec 2021 22:08:27: 5000000 INFO @ Wed, 08 Dec 2021 22:08:34: 2000000 INFO @ Wed, 08 Dec 2021 22:08:35: 6000000 INFO @ Wed, 08 Dec 2021 22:08:42: 3000000 INFO @ Wed, 08 Dec 2021 22:08:43: 7000000 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 22:08:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120620/SRX9120620.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120620/SRX9120620.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120620/SRX9120620.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120620/SRX9120620.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 22:08:47: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:08:47: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:08:49: 4000000 INFO @ Wed, 08 Dec 2021 22:08:52: 8000000 INFO @ Wed, 08 Dec 2021 22:08:54: 1000000 INFO @ Wed, 08 Dec 2021 22:08:58: 5000000 INFO @ Wed, 08 Dec 2021 22:09:01: 9000000 INFO @ Wed, 08 Dec 2021 22:09:01: 2000000 INFO @ Wed, 08 Dec 2021 22:09:06: 6000000 INFO @ Wed, 08 Dec 2021 22:09:09: 10000000 INFO @ Wed, 08 Dec 2021 22:09:09: 3000000 INFO @ Wed, 08 Dec 2021 22:09:14: 7000000 INFO @ Wed, 08 Dec 2021 22:09:16: 4000000 INFO @ Wed, 08 Dec 2021 22:09:17: 11000000 INFO @ Wed, 08 Dec 2021 22:09:23: 8000000 INFO @ Wed, 08 Dec 2021 22:09:23: 5000000 INFO @ Wed, 08 Dec 2021 22:09:26: 12000000 INFO @ Wed, 08 Dec 2021 22:09:30: 6000000 INFO @ Wed, 08 Dec 2021 22:09:31: 9000000 INFO @ Wed, 08 Dec 2021 22:09:35: 13000000 INFO @ Wed, 08 Dec 2021 22:09:37: 7000000 INFO @ Wed, 08 Dec 2021 22:09:40: 10000000 INFO @ Wed, 08 Dec 2021 22:09:43: 14000000 INFO @ Wed, 08 Dec 2021 22:09:45: 8000000 INFO @ Wed, 08 Dec 2021 22:09:49: 11000000 INFO @ Wed, 08 Dec 2021 22:09:54: 15000000 INFO @ Wed, 08 Dec 2021 22:09:56: 9000000 INFO @ Wed, 08 Dec 2021 22:10:00: 12000000 INFO @ Wed, 08 Dec 2021 22:10:04: 10000000 INFO @ Wed, 08 Dec 2021 22:10:04: 16000000 INFO @ Wed, 08 Dec 2021 22:10:10: 13000000 INFO @ Wed, 08 Dec 2021 22:10:12: 11000000 INFO @ Wed, 08 Dec 2021 22:10:13: 17000000 INFO @ Wed, 08 Dec 2021 22:10:19: 14000000 INFO @ Wed, 08 Dec 2021 22:10:20: 12000000 INFO @ Wed, 08 Dec 2021 22:10:22: 18000000 INFO @ Wed, 08 Dec 2021 22:10:27: 15000000 INFO @ Wed, 08 Dec 2021 22:10:28: 13000000 INFO @ Wed, 08 Dec 2021 22:10:31: 19000000 INFO @ Wed, 08 Dec 2021 22:10:34: 14000000 INFO @ Wed, 08 Dec 2021 22:10:36: 16000000 INFO @ Wed, 08 Dec 2021 22:10:39: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 22:10:39: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 22:10:39: #1 total tags in treatment: 19983855 INFO @ Wed, 08 Dec 2021 22:10:39: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:10:39: #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 22:10:39: #1 tags after filtering in treatment: 19983855 INFO @ Wed, 08 Dec 2021 22:10:39: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:10:39: #1 finished! INFO @ Wed, 08 Dec 2021 22:10:39: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:10:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:10:40: 15000000 INFO @ Wed, 08 Dec 2021 22:10:41: #2 number of paired peaks: 185 WARNING @ Wed, 08 Dec 2021 22:10:41: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Wed, 08 Dec 2021 22:10:41: start model_add_line... INFO @ Wed, 08 Dec 2021 22:10:41: start X-correlation... INFO @ Wed, 08 Dec 2021 22:10:41: end of X-cor INFO @ Wed, 08 Dec 2021 22:10:41: #2 finished! INFO @ Wed, 08 Dec 2021 22:10:41: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 22:10:41: #2 alternative fragment length(s) may be 1,29,48,528,532,557 bps INFO @ Wed, 08 Dec 2021 22:10:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120620/SRX9120620.05_model.r WARNING @ Wed, 08 Dec 2021 22:10:41: #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 22:10:41: #2 You may need to consider one of the other alternative d(s): 1,29,48,528,532,557 WARNING @ Wed, 08 Dec 2021 22:10:41: #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 22:10:41: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:10:41: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:10:45: 17000000 INFO @ Wed, 08 Dec 2021 22:10:48: 16000000 INFO @ Wed, 08 Dec 2021 22:10:54: 18000000 INFO @ Wed, 08 Dec 2021 22:10:54: 17000000 INFO @ Wed, 08 Dec 2021 22:11:00: 18000000 INFO @ Wed, 08 Dec 2021 22:11:02: 19000000 INFO @ Wed, 08 Dec 2021 22:11:07: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 22:11:11: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 22:11:11: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 22:11:11: #1 total tags in treatment: 19983855 INFO @ Wed, 08 Dec 2021 22:11:11: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:11:11: #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 22:11:11: #1 tags after filtering in treatment: 19983855 INFO @ Wed, 08 Dec 2021 22:11:11: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:11:11: #1 finished! INFO @ Wed, 08 Dec 2021 22:11:11: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:11:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:11:11: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:11:12: #2 number of paired peaks: 185 WARNING @ Wed, 08 Dec 2021 22:11:12: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Wed, 08 Dec 2021 22:11:12: start model_add_line... INFO @ Wed, 08 Dec 2021 22:11:13: start X-correlation... INFO @ Wed, 08 Dec 2021 22:11:13: end of X-cor INFO @ Wed, 08 Dec 2021 22:11:13: #2 finished! INFO @ Wed, 08 Dec 2021 22:11:13: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 22:11:13: #2 alternative fragment length(s) may be 1,29,48,528,532,557 bps INFO @ Wed, 08 Dec 2021 22:11:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120620/SRX9120620.10_model.r WARNING @ Wed, 08 Dec 2021 22:11:13: #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 22:11:13: #2 You may need to consider one of the other alternative d(s): 1,29,48,528,532,557 WARNING @ Wed, 08 Dec 2021 22:11:13: #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 22:11:13: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:11:13: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:11:13: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 22:11:13: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 22:11:13: #1 total tags in treatment: 19983855 INFO @ Wed, 08 Dec 2021 22:11:13: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:11:13: #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 22:11:14: #1 tags after filtering in treatment: 19983855 INFO @ Wed, 08 Dec 2021 22:11:14: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:11:14: #1 finished! INFO @ Wed, 08 Dec 2021 22:11:14: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:11:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:11:15: #2 number of paired peaks: 185 WARNING @ Wed, 08 Dec 2021 22:11:15: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Wed, 08 Dec 2021 22:11:15: start model_add_line... INFO @ Wed, 08 Dec 2021 22:11:15: start X-correlation... INFO @ Wed, 08 Dec 2021 22:11:15: end of X-cor INFO @ Wed, 08 Dec 2021 22:11:15: #2 finished! INFO @ Wed, 08 Dec 2021 22:11:15: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 22:11:15: #2 alternative fragment length(s) may be 1,29,48,528,532,557 bps INFO @ Wed, 08 Dec 2021 22:11:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120620/SRX9120620.20_model.r WARNING @ Wed, 08 Dec 2021 22:11:15: #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 22:11:15: #2 You may need to consider one of the other alternative d(s): 1,29,48,528,532,557 WARNING @ Wed, 08 Dec 2021 22:11:15: #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 22:11:15: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:11:15: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:11:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120620/SRX9120620.05_peaks.xls INFO @ Wed, 08 Dec 2021 22:11:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120620/SRX9120620.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:11:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120620/SRX9120620.05_summits.bed INFO @ Wed, 08 Dec 2021 22:11:30: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:11:43: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:11:44: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:11:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120620/SRX9120620.10_peaks.xls INFO @ Wed, 08 Dec 2021 22:11:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120620/SRX9120620.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:11:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120620/SRX9120620.10_summits.bed INFO @ Wed, 08 Dec 2021 22:11:59: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:12:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120620/SRX9120620.20_peaks.xls INFO @ Wed, 08 Dec 2021 22:12:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120620/SRX9120620.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:12:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120620/SRX9120620.20_summits.bed INFO @ Wed, 08 Dec 2021 22:12:00: 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。