Job ID = 10165961 SRX = SRX8331144 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: 00:11:19 32320233 reads; of these: 32320233 (100.00%) were unpaired; of these: 298544 (0.92%) aligned 0 times 27082777 (83.80%) aligned exactly 1 time 4938912 (15.28%) aligned >1 times 99.08% overall alignment rate Time searching: 00:11:19 Overall time: 00:11:19 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 16 files... [bam_rmdupse_core] 23414147 / 32021689 = 0.7312 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 20:36:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8331144/SRX8331144.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8331144/SRX8331144.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8331144/SRX8331144.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8331144/SRX8331144.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 20:36:02: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:36:02: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:36:08: 1000000 INFO @ Thu, 08 Oct 2020 20:36:15: 2000000 INFO @ Thu, 08 Oct 2020 20:36:21: 3000000 INFO @ Thu, 08 Oct 2020 20:36:28: 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 20:36:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8331144/SRX8331144.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8331144/SRX8331144.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8331144/SRX8331144.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8331144/SRX8331144.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 20:36:32: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:36:32: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:36:35: 5000000 INFO @ Thu, 08 Oct 2020 20:36:40: 1000000 INFO @ Thu, 08 Oct 2020 20:36:43: 6000000 INFO @ Thu, 08 Oct 2020 20:36:47: 2000000 INFO @ Thu, 08 Oct 2020 20:36:50: 7000000 INFO @ Thu, 08 Oct 2020 20:36:55: 3000000 INFO @ Thu, 08 Oct 2020 20:36:58: 8000000 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 20:37:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8331144/SRX8331144.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8331144/SRX8331144.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8331144/SRX8331144.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8331144/SRX8331144.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 20:37:02: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:37:02: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:37:02: #1 tag size is determined as 74 bps INFO @ Thu, 08 Oct 2020 20:37:02: #1 tag size = 74 INFO @ Thu, 08 Oct 2020 20:37:02: #1 total tags in treatment: 8607542 INFO @ Thu, 08 Oct 2020 20:37:02: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:37:02: #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 20:37:02: #1 tags after filtering in treatment: 8607542 INFO @ Thu, 08 Oct 2020 20:37:02: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:37:02: #1 finished! INFO @ Thu, 08 Oct 2020 20:37:02: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:37:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:37:03: #2 number of paired peaks: 587 WARNING @ Thu, 08 Oct 2020 20:37:03: Fewer paired peaks (587) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 587 pairs to build model! INFO @ Thu, 08 Oct 2020 20:37:03: start model_add_line... INFO @ Thu, 08 Oct 2020 20:37:03: start X-correlation... INFO @ Thu, 08 Oct 2020 20:37:03: end of X-cor INFO @ Thu, 08 Oct 2020 20:37:03: #2 finished! INFO @ Thu, 08 Oct 2020 20:37:03: #2 predicted fragment length is 58 bps INFO @ Thu, 08 Oct 2020 20:37:03: #2 alternative fragment length(s) may be 3,58,582,598 bps INFO @ Thu, 08 Oct 2020 20:37:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8331144/SRX8331144.05_model.r INFO @ Thu, 08 Oct 2020 20:37:03: 4000000 WARNING @ Thu, 08 Oct 2020 20:37:03: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:37:03: #2 You may need to consider one of the other alternative d(s): 3,58,582,598 WARNING @ Thu, 08 Oct 2020 20:37:03: #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 20:37:03: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:37:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:37:09: 1000000 INFO @ Thu, 08 Oct 2020 20:37:11: 5000000 INFO @ Thu, 08 Oct 2020 20:37:17: 2000000 INFO @ Thu, 08 Oct 2020 20:37:18: 6000000 INFO @ Thu, 08 Oct 2020 20:37:21: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:37:24: 3000000 INFO @ Thu, 08 Oct 2020 20:37:26: 7000000 INFO @ Thu, 08 Oct 2020 20:37:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8331144/SRX8331144.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:37:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8331144/SRX8331144.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:37:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8331144/SRX8331144.05_summits.bed INFO @ Thu, 08 Oct 2020 20:37:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (897 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:37:32: 4000000 INFO @ Thu, 08 Oct 2020 20:37:34: 8000000 INFO @ Thu, 08 Oct 2020 20:37:38: #1 tag size is determined as 74 bps INFO @ Thu, 08 Oct 2020 20:37:38: #1 tag size = 74 INFO @ Thu, 08 Oct 2020 20:37:38: #1 total tags in treatment: 8607542 INFO @ Thu, 08 Oct 2020 20:37:38: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:37:38: #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 20:37:38: #1 tags after filtering in treatment: 8607542 INFO @ Thu, 08 Oct 2020 20:37:38: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:37:38: #1 finished! INFO @ Thu, 08 Oct 2020 20:37:38: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:37:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:37:39: #2 number of paired peaks: 587 WARNING @ Thu, 08 Oct 2020 20:37:39: Fewer paired peaks (587) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 587 pairs to build model! INFO @ Thu, 08 Oct 2020 20:37:39: start model_add_line... INFO @ Thu, 08 Oct 2020 20:37:39: start X-correlation... INFO @ Thu, 08 Oct 2020 20:37:39: end of X-cor INFO @ Thu, 08 Oct 2020 20:37:39: #2 finished! INFO @ Thu, 08 Oct 2020 20:37:39: #2 predicted fragment length is 58 bps INFO @ Thu, 08 Oct 2020 20:37:39: #2 alternative fragment length(s) may be 3,58,582,598 bps INFO @ Thu, 08 Oct 2020 20:37:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8331144/SRX8331144.10_model.r WARNING @ Thu, 08 Oct 2020 20:37:39: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:37:39: #2 You may need to consider one of the other alternative d(s): 3,58,582,598 WARNING @ Thu, 08 Oct 2020 20:37:39: #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 20:37:39: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:37:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:37:39: 5000000 INFO @ Thu, 08 Oct 2020 20:37:46: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:37:53: 7000000 INFO @ Thu, 08 Oct 2020 20:37:56: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:38:00: 8000000 INFO @ Thu, 08 Oct 2020 20:38:04: #1 tag size is determined as 74 bps INFO @ Thu, 08 Oct 2020 20:38:04: #1 tag size = 74 INFO @ Thu, 08 Oct 2020 20:38:04: #1 total tags in treatment: 8607542 INFO @ Thu, 08 Oct 2020 20:38:04: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:38:04: #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 20:38:04: #1 tags after filtering in treatment: 8607542 INFO @ Thu, 08 Oct 2020 20:38:04: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:38:04: #1 finished! INFO @ Thu, 08 Oct 2020 20:38:04: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:38:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:38:05: #2 number of paired peaks: 587 WARNING @ Thu, 08 Oct 2020 20:38:05: Fewer paired peaks (587) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 587 pairs to build model! INFO @ Thu, 08 Oct 2020 20:38:05: start model_add_line... INFO @ Thu, 08 Oct 2020 20:38:05: start X-correlation... INFO @ Thu, 08 Oct 2020 20:38:05: end of X-cor INFO @ Thu, 08 Oct 2020 20:38:05: #2 finished! INFO @ Thu, 08 Oct 2020 20:38:05: #2 predicted fragment length is 58 bps INFO @ Thu, 08 Oct 2020 20:38:05: #2 alternative fragment length(s) may be 3,58,582,598 bps INFO @ Thu, 08 Oct 2020 20:38:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8331144/SRX8331144.20_model.r WARNING @ Thu, 08 Oct 2020 20:38:05: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:38:05: #2 You may need to consider one of the other alternative d(s): 3,58,582,598 WARNING @ Thu, 08 Oct 2020 20:38:05: #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 20:38:05: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:38:05: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:38:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8331144/SRX8331144.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:38:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8331144/SRX8331144.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:38:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8331144/SRX8331144.10_summits.bed INFO @ Thu, 08 Oct 2020 20:38:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (557 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:38:23: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:38:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8331144/SRX8331144.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:38:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8331144/SRX8331144.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:38:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8331144/SRX8331144.20_summits.bed INFO @ Thu, 08 Oct 2020 20:38:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (278 records, 4 fields): 1 millis CompletedMACS2peakCalling