Job ID = 10166096 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: 00:00:00 Multiseed full-index search: 00:05:39 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: 00:05:39 Overall time: 00:05:39 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:40:19: # 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 @ Thu, 08 Oct 2020 20:40:19: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:40:19: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:40:24: 1000000 INFO @ Thu, 08 Oct 2020 20:40:30: 2000000 INFO @ Thu, 08 Oct 2020 20:40:36: 3000000 INFO @ Thu, 08 Oct 2020 20:40:42: 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 20:40:48: 5000000 INFO @ Thu, 08 Oct 2020 20:40:49: # 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 @ Thu, 08 Oct 2020 20:40:49: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:40:49: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:40:54: 6000000 INFO @ Thu, 08 Oct 2020 20:40:55: 1000000 INFO @ Thu, 08 Oct 2020 20:41:00: 7000000 INFO @ Thu, 08 Oct 2020 20:41:01: 2000000 INFO @ Thu, 08 Oct 2020 20:41:06: 8000000 INFO @ Thu, 08 Oct 2020 20:41:08: 3000000 INFO @ Thu, 08 Oct 2020 20:41:13: 9000000 INFO @ Thu, 08 Oct 2020 20:41:14: 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 @ Thu, 08 Oct 2020 20:41:19: 10000000 INFO @ Thu, 08 Oct 2020 20:41:19: # 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 @ Thu, 08 Oct 2020 20:41:19: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:41:19: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:41:20: 5000000 INFO @ Thu, 08 Oct 2020 20:41:25: 11000000 INFO @ Thu, 08 Oct 2020 20:41:26: 1000000 INFO @ Thu, 08 Oct 2020 20:41:27: 6000000 INFO @ Thu, 08 Oct 2020 20:41:31: 12000000 INFO @ Thu, 08 Oct 2020 20:41:32: 2000000 INFO @ Thu, 08 Oct 2020 20:41:33: 7000000 INFO @ Thu, 08 Oct 2020 20:41:37: 13000000 INFO @ Thu, 08 Oct 2020 20:41:38: 3000000 INFO @ Thu, 08 Oct 2020 20:41:39: 8000000 INFO @ Thu, 08 Oct 2020 20:41:43: 14000000 INFO @ Thu, 08 Oct 2020 20:41:45: 4000000 INFO @ Thu, 08 Oct 2020 20:41:45: 9000000 INFO @ Thu, 08 Oct 2020 20:41:49: 15000000 INFO @ Thu, 08 Oct 2020 20:41:51: 5000000 INFO @ Thu, 08 Oct 2020 20:41:52: 10000000 INFO @ Thu, 08 Oct 2020 20:41:55: 16000000 INFO @ Thu, 08 Oct 2020 20:41:58: 6000000 INFO @ Thu, 08 Oct 2020 20:41:58: 11000000 INFO @ Thu, 08 Oct 2020 20:42:02: 17000000 INFO @ Thu, 08 Oct 2020 20:42:04: 7000000 INFO @ Thu, 08 Oct 2020 20:42:04: 12000000 INFO @ Thu, 08 Oct 2020 20:42:08: 18000000 INFO @ Thu, 08 Oct 2020 20:42:10: 8000000 INFO @ Thu, 08 Oct 2020 20:42:11: 13000000 INFO @ Thu, 08 Oct 2020 20:42:14: 19000000 INFO @ Thu, 08 Oct 2020 20:42:17: 9000000 INFO @ Thu, 08 Oct 2020 20:42:17: 14000000 INFO @ Thu, 08 Oct 2020 20:42:20: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:42:20: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:42:20: #1 total tags in treatment: 19983855 INFO @ Thu, 08 Oct 2020 20:42:20: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:42:20: #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 20:42:21: #1 tags after filtering in treatment: 19983855 INFO @ Thu, 08 Oct 2020 20:42:21: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:42:21: #1 finished! INFO @ Thu, 08 Oct 2020 20:42:21: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:42:21: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:42:22: #2 number of paired peaks: 185 WARNING @ Thu, 08 Oct 2020 20:42:22: 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 @ Thu, 08 Oct 2020 20:42:22: start model_add_line... INFO @ Thu, 08 Oct 2020 20:42:22: start X-correlation... INFO @ Thu, 08 Oct 2020 20:42:22: end of X-cor INFO @ Thu, 08 Oct 2020 20:42:22: #2 finished! INFO @ Thu, 08 Oct 2020 20:42:22: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:42:22: #2 alternative fragment length(s) may be 1,29,48,528,532,557 bps INFO @ Thu, 08 Oct 2020 20:42:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120620/SRX9120620.05_model.r WARNING @ Thu, 08 Oct 2020 20:42:22: #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 20:42:22: #2 You may need to consider one of the other alternative d(s): 1,29,48,528,532,557 WARNING @ Thu, 08 Oct 2020 20:42:22: #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 20:42:22: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:42:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:42:23: 10000000 INFO @ Thu, 08 Oct 2020 20:42:23: 15000000 INFO @ Thu, 08 Oct 2020 20:42:29: 11000000 INFO @ Thu, 08 Oct 2020 20:42:30: 16000000 INFO @ Thu, 08 Oct 2020 20:42:35: 12000000 INFO @ Thu, 08 Oct 2020 20:42:36: 17000000 INFO @ Thu, 08 Oct 2020 20:42:41: 13000000 INFO @ Thu, 08 Oct 2020 20:42:42: 18000000 INFO @ Thu, 08 Oct 2020 20:42:48: 14000000 INFO @ Thu, 08 Oct 2020 20:42:48: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:42:54: 15000000 INFO @ Thu, 08 Oct 2020 20:42:54: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:42:54: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:42:54: #1 total tags in treatment: 19983855 INFO @ Thu, 08 Oct 2020 20:42:54: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:42:54: #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 20:42:55: #1 tags after filtering in treatment: 19983855 INFO @ Thu, 08 Oct 2020 20:42:55: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:42:55: #1 finished! INFO @ Thu, 08 Oct 2020 20:42:55: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:42:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:42:55: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:42:56: #2 number of paired peaks: 185 WARNING @ Thu, 08 Oct 2020 20:42:56: 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 @ Thu, 08 Oct 2020 20:42:56: start model_add_line... INFO @ Thu, 08 Oct 2020 20:42:56: start X-correlation... INFO @ Thu, 08 Oct 2020 20:42:56: end of X-cor INFO @ Thu, 08 Oct 2020 20:42:56: #2 finished! INFO @ Thu, 08 Oct 2020 20:42:56: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:42:56: #2 alternative fragment length(s) may be 1,29,48,528,532,557 bps INFO @ Thu, 08 Oct 2020 20:42:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120620/SRX9120620.10_model.r WARNING @ Thu, 08 Oct 2020 20:42:56: #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 20:42:56: #2 You may need to consider one of the other alternative d(s): 1,29,48,528,532,557 WARNING @ Thu, 08 Oct 2020 20:42:56: #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 20:42:56: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:42:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:43:00: 16000000 INFO @ Thu, 08 Oct 2020 20:43:05: 17000000 INFO @ Thu, 08 Oct 2020 20:43:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120620/SRX9120620.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:43:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120620/SRX9120620.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:43:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120620/SRX9120620.05_summits.bed INFO @ Thu, 08 Oct 2020 20:43:11: Done! INFO @ Thu, 08 Oct 2020 20:43:11: 18000000 pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:43:17: 19000000 INFO @ Thu, 08 Oct 2020 20:43:23: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:43:23: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:43:23: #1 total tags in treatment: 19983855 INFO @ Thu, 08 Oct 2020 20:43:23: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:43:23: #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 20:43:23: #1 tags after filtering in treatment: 19983855 INFO @ Thu, 08 Oct 2020 20:43:23: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:43:23: #1 finished! INFO @ Thu, 08 Oct 2020 20:43:23: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:43:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:43:24: #2 number of paired peaks: 185 WARNING @ Thu, 08 Oct 2020 20:43:24: 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 @ Thu, 08 Oct 2020 20:43:24: start model_add_line... INFO @ Thu, 08 Oct 2020 20:43:24: start X-correlation... INFO @ Thu, 08 Oct 2020 20:43:24: end of X-cor INFO @ Thu, 08 Oct 2020 20:43:24: #2 finished! INFO @ Thu, 08 Oct 2020 20:43:24: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:43:24: #2 alternative fragment length(s) may be 1,29,48,528,532,557 bps INFO @ Thu, 08 Oct 2020 20:43:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120620/SRX9120620.20_model.r WARNING @ Thu, 08 Oct 2020 20:43:24: #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 20:43:24: #2 You may need to consider one of the other alternative d(s): 1,29,48,528,532,557 WARNING @ Thu, 08 Oct 2020 20:43:24: #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 20:43:24: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:43:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:43:30: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:43:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120620/SRX9120620.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:43:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120620/SRX9120620.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:43:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120620/SRX9120620.10_summits.bed INFO @ Thu, 08 Oct 2020 20:43:45: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:43:58: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:44:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120620/SRX9120620.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:44:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120620/SRX9120620.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:44:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120620/SRX9120620.20_summits.bed INFO @ Thu, 08 Oct 2020 20:44:14: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling