Job ID = 10166095 SRX = SRX9120613 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: 00:06:19 37768674 reads; of these: 37768674 (100.00%) were unpaired; of these: 12273079 (32.50%) aligned 0 times 21159682 (56.02%) aligned exactly 1 time 4335913 (11.48%) aligned >1 times 67.50% overall alignment rate Time searching: 00:06:19 Overall time: 00:06:19 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] 4316710 / 25495595 = 0.1693 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 20:41:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.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 20:41:01: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:41:01: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:41:07: 1000000 INFO @ Thu, 08 Oct 2020 20:41:12: 2000000 INFO @ Thu, 08 Oct 2020 20:41:17: 3000000 INFO @ Thu, 08 Oct 2020 20:41:23: 4000000 INFO @ Thu, 08 Oct 2020 20:41:28: 5000000 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 20:41:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.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 20:41:31: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:41:31: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:41:34: 6000000 INFO @ Thu, 08 Oct 2020 20:41:37: 1000000 INFO @ Thu, 08 Oct 2020 20:41:40: 7000000 INFO @ Thu, 08 Oct 2020 20:41:42: 2000000 INFO @ Thu, 08 Oct 2020 20:41:45: 8000000 INFO @ Thu, 08 Oct 2020 20:41:48: 3000000 INFO @ Thu, 08 Oct 2020 20:41:51: 9000000 INFO @ Thu, 08 Oct 2020 20:41:54: 4000000 INFO @ Thu, 08 Oct 2020 20:41:57: 10000000 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 20:42:00: 5000000 INFO @ Thu, 08 Oct 2020 20:42:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.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 20:42:01: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:42:01: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:42:03: 11000000 INFO @ Thu, 08 Oct 2020 20:42:06: 6000000 INFO @ Thu, 08 Oct 2020 20:42:07: 1000000 INFO @ Thu, 08 Oct 2020 20:42:09: 12000000 INFO @ Thu, 08 Oct 2020 20:42:12: 7000000 INFO @ Thu, 08 Oct 2020 20:42:13: 2000000 INFO @ Thu, 08 Oct 2020 20:42:14: 13000000 INFO @ Thu, 08 Oct 2020 20:42:18: 8000000 INFO @ Thu, 08 Oct 2020 20:42:19: 3000000 INFO @ Thu, 08 Oct 2020 20:42:20: 14000000 INFO @ Thu, 08 Oct 2020 20:42:23: 9000000 INFO @ Thu, 08 Oct 2020 20:42:25: 4000000 INFO @ Thu, 08 Oct 2020 20:42:26: 15000000 INFO @ Thu, 08 Oct 2020 20:42:29: 10000000 INFO @ Thu, 08 Oct 2020 20:42:30: 5000000 INFO @ Thu, 08 Oct 2020 20:42:32: 16000000 INFO @ Thu, 08 Oct 2020 20:42:35: 11000000 INFO @ Thu, 08 Oct 2020 20:42:36: 6000000 INFO @ Thu, 08 Oct 2020 20:42:38: 17000000 INFO @ Thu, 08 Oct 2020 20:42:41: 12000000 INFO @ Thu, 08 Oct 2020 20:42:42: 7000000 INFO @ Thu, 08 Oct 2020 20:42:44: 18000000 INFO @ Thu, 08 Oct 2020 20:42:47: 13000000 INFO @ Thu, 08 Oct 2020 20:42:48: 8000000 INFO @ Thu, 08 Oct 2020 20:42:50: 19000000 INFO @ Thu, 08 Oct 2020 20:42:53: 14000000 INFO @ Thu, 08 Oct 2020 20:42:54: 9000000 INFO @ Thu, 08 Oct 2020 20:42:56: 20000000 INFO @ Thu, 08 Oct 2020 20:42:58: 15000000 INFO @ Thu, 08 Oct 2020 20:43:00: 10000000 INFO @ Thu, 08 Oct 2020 20:43:01: 21000000 INFO @ Thu, 08 Oct 2020 20:43:02: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:43:02: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:43:02: #1 total tags in treatment: 21178885 INFO @ Thu, 08 Oct 2020 20:43:02: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:43:02: #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 20:43:03: #1 tags after filtering in treatment: 21178885 INFO @ Thu, 08 Oct 2020 20:43:03: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:43:03: #1 finished! INFO @ Thu, 08 Oct 2020 20:43:03: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:43:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:43:04: #2 number of paired peaks: 195 WARNING @ Thu, 08 Oct 2020 20:43:04: Fewer paired peaks (195) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 195 pairs to build model! INFO @ Thu, 08 Oct 2020 20:43:04: start model_add_line... INFO @ Thu, 08 Oct 2020 20:43:04: start X-correlation... INFO @ Thu, 08 Oct 2020 20:43:04: end of X-cor INFO @ Thu, 08 Oct 2020 20:43:04: #2 finished! INFO @ Thu, 08 Oct 2020 20:43:04: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:43:04: #2 alternative fragment length(s) may be 1,26,595 bps INFO @ Thu, 08 Oct 2020 20:43:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.05_model.r WARNING @ Thu, 08 Oct 2020 20:43:04: #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 20:43:04: #2 You may need to consider one of the other alternative d(s): 1,26,595 WARNING @ Thu, 08 Oct 2020 20:43:04: #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 20:43:04: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:43:04: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:43:04: 16000000 INFO @ Thu, 08 Oct 2020 20:43:05: 11000000 INFO @ Thu, 08 Oct 2020 20:43:10: 17000000 INFO @ Thu, 08 Oct 2020 20:43:11: 12000000 INFO @ Thu, 08 Oct 2020 20:43:16: 18000000 INFO @ Thu, 08 Oct 2020 20:43:17: 13000000 INFO @ Thu, 08 Oct 2020 20:43:22: 19000000 INFO @ Thu, 08 Oct 2020 20:43:23: 14000000 INFO @ Thu, 08 Oct 2020 20:43:27: 20000000 INFO @ Thu, 08 Oct 2020 20:43:28: 15000000 INFO @ Thu, 08 Oct 2020 20:43:33: 21000000 INFO @ Thu, 08 Oct 2020 20:43:34: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:43:34: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:43:34: #1 total tags in treatment: 21178885 INFO @ Thu, 08 Oct 2020 20:43:34: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:43:34: #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 20:43:34: #1 tags after filtering in treatment: 21178885 INFO @ Thu, 08 Oct 2020 20:43:34: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:43:34: #1 finished! INFO @ Thu, 08 Oct 2020 20:43:34: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:43:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:43:34: 16000000 INFO @ Thu, 08 Oct 2020 20:43:35: #2 number of paired peaks: 195 WARNING @ Thu, 08 Oct 2020 20:43:35: Fewer paired peaks (195) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 195 pairs to build model! INFO @ Thu, 08 Oct 2020 20:43:35: start model_add_line... INFO @ Thu, 08 Oct 2020 20:43:36: start X-correlation... INFO @ Thu, 08 Oct 2020 20:43:36: end of X-cor INFO @ Thu, 08 Oct 2020 20:43:36: #2 finished! INFO @ Thu, 08 Oct 2020 20:43:36: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:43:36: #2 alternative fragment length(s) may be 1,26,595 bps INFO @ Thu, 08 Oct 2020 20:43:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.10_model.r WARNING @ Thu, 08 Oct 2020 20:43:36: #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 20:43:36: #2 You may need to consider one of the other alternative d(s): 1,26,595 WARNING @ Thu, 08 Oct 2020 20:43:36: #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 20:43:36: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:43:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:43:37: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:43:40: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:43:46: 18000000 INFO @ Thu, 08 Oct 2020 20:43:52: 19000000 INFO @ Thu, 08 Oct 2020 20:43:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:43:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:43:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.05_summits.bed INFO @ Thu, 08 Oct 2020 20:43:53: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:43:57: 20000000 INFO @ Thu, 08 Oct 2020 20:44:03: 21000000 INFO @ Thu, 08 Oct 2020 20:44:04: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:44:04: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:44:04: #1 total tags in treatment: 21178885 INFO @ Thu, 08 Oct 2020 20:44:04: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:44:04: #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 20:44:04: #1 tags after filtering in treatment: 21178885 INFO @ Thu, 08 Oct 2020 20:44:04: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:44:04: #1 finished! INFO @ Thu, 08 Oct 2020 20:44:04: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:44:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:44:05: #2 number of paired peaks: 195 WARNING @ Thu, 08 Oct 2020 20:44:05: Fewer paired peaks (195) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 195 pairs to build model! INFO @ Thu, 08 Oct 2020 20:44:05: start model_add_line... INFO @ Thu, 08 Oct 2020 20:44:05: start X-correlation... INFO @ Thu, 08 Oct 2020 20:44:05: end of X-cor INFO @ Thu, 08 Oct 2020 20:44:05: #2 finished! INFO @ Thu, 08 Oct 2020 20:44:05: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:44:05: #2 alternative fragment length(s) may be 1,26,595 bps INFO @ Thu, 08 Oct 2020 20:44:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.20_model.r WARNING @ Thu, 08 Oct 2020 20:44:05: #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 20:44:05: #2 You may need to consider one of the other alternative d(s): 1,26,595 WARNING @ Thu, 08 Oct 2020 20:44:05: #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 20:44:05: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:44:05: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:44:09: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:44:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:44:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:44:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.10_summits.bed INFO @ Thu, 08 Oct 2020 20:44:24: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:44:38: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:44:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:44:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:44:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9120613/SRX9120613.20_summits.bed INFO @ Thu, 08 Oct 2020 20:44:54: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling