Job ID = 16435505 SRX = SRX13110321 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: 00:04:23 19007906 reads; of these: 19007906 (100.00%) were unpaired; of these: 9461778 (49.78%) aligned 0 times 8042500 (42.31%) aligned exactly 1 time 1503628 (7.91%) aligned >1 times 50.22% overall alignment rate Time searching: 00:04:23 Overall time: 00:04:23 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_rmdupse_core] 835438 / 9546128 = 0.0875 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:51:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110321/SRX13110321.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110321/SRX13110321.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110321/SRX13110321.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110321/SRX13110321.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 @ Tue, 02 Aug 2022 10:51:07: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:51:07: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:51:14: 1000000 INFO @ Tue, 02 Aug 2022 10:51:21: 2000000 INFO @ Tue, 02 Aug 2022 10:51:28: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:51:35: 4000000 INFO @ Tue, 02 Aug 2022 10:51:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110321/SRX13110321.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110321/SRX13110321.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110321/SRX13110321.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110321/SRX13110321.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 @ Tue, 02 Aug 2022 10:51:36: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:51:36: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:51:43: 1000000 INFO @ Tue, 02 Aug 2022 10:51:43: 5000000 INFO @ Tue, 02 Aug 2022 10:51:50: 2000000 INFO @ Tue, 02 Aug 2022 10:51:51: 6000000 INFO @ Tue, 02 Aug 2022 10:51:57: 3000000 INFO @ Tue, 02 Aug 2022 10:51:58: 7000000 INFO @ Tue, 02 Aug 2022 10:52:04: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:52:06: 8000000 INFO @ Tue, 02 Aug 2022 10:52:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110321/SRX13110321.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110321/SRX13110321.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110321/SRX13110321.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110321/SRX13110321.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 @ Tue, 02 Aug 2022 10:52:06: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:52:06: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:52:11: 5000000 INFO @ Tue, 02 Aug 2022 10:52:11: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:52:11: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:52:11: #1 total tags in treatment: 8710690 INFO @ Tue, 02 Aug 2022 10:52:11: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:52:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:52:11: #1 tags after filtering in treatment: 8710690 INFO @ Tue, 02 Aug 2022 10:52:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:52:11: #1 finished! INFO @ Tue, 02 Aug 2022 10:52:11: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:52:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:52:12: #2 number of paired peaks: 308 WARNING @ Tue, 02 Aug 2022 10:52:12: Fewer paired peaks (308) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 308 pairs to build model! INFO @ Tue, 02 Aug 2022 10:52:12: start model_add_line... INFO @ Tue, 02 Aug 2022 10:52:12: start X-correlation... INFO @ Tue, 02 Aug 2022 10:52:12: end of X-cor INFO @ Tue, 02 Aug 2022 10:52:12: #2 finished! INFO @ Tue, 02 Aug 2022 10:52:12: #2 predicted fragment length is 74 bps INFO @ Tue, 02 Aug 2022 10:52:12: #2 alternative fragment length(s) may be 4,74,562,598 bps INFO @ Tue, 02 Aug 2022 10:52:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110321/SRX13110321.05_model.r WARNING @ Tue, 02 Aug 2022 10:52:12: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:52:12: #2 You may need to consider one of the other alternative d(s): 4,74,562,598 WARNING @ Tue, 02 Aug 2022 10:52:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:52:12: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:52:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:52:13: 1000000 INFO @ Tue, 02 Aug 2022 10:52:17: 6000000 INFO @ Tue, 02 Aug 2022 10:52:20: 2000000 INFO @ Tue, 02 Aug 2022 10:52:24: 7000000 INFO @ Tue, 02 Aug 2022 10:52:27: 3000000 INFO @ Tue, 02 Aug 2022 10:52:30: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:52:31: 8000000 INFO @ Tue, 02 Aug 2022 10:52:33: 4000000 INFO @ Tue, 02 Aug 2022 10:52:36: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:52:36: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:52:36: #1 total tags in treatment: 8710690 INFO @ Tue, 02 Aug 2022 10:52:36: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:52:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:52:36: #1 tags after filtering in treatment: 8710690 INFO @ Tue, 02 Aug 2022 10:52:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:52:36: #1 finished! INFO @ Tue, 02 Aug 2022 10:52:36: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:52:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:52:36: #2 number of paired peaks: 308 WARNING @ Tue, 02 Aug 2022 10:52:36: Fewer paired peaks (308) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 308 pairs to build model! INFO @ Tue, 02 Aug 2022 10:52:36: start model_add_line... INFO @ Tue, 02 Aug 2022 10:52:37: start X-correlation... INFO @ Tue, 02 Aug 2022 10:52:37: end of X-cor INFO @ Tue, 02 Aug 2022 10:52:37: #2 finished! INFO @ Tue, 02 Aug 2022 10:52:37: #2 predicted fragment length is 74 bps INFO @ Tue, 02 Aug 2022 10:52:37: #2 alternative fragment length(s) may be 4,74,562,598 bps INFO @ Tue, 02 Aug 2022 10:52:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110321/SRX13110321.10_model.r WARNING @ Tue, 02 Aug 2022 10:52:37: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:52:37: #2 You may need to consider one of the other alternative d(s): 4,74,562,598 WARNING @ Tue, 02 Aug 2022 10:52:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:52:37: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:52:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:52:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110321/SRX13110321.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:52:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110321/SRX13110321.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:52:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110321/SRX13110321.05_summits.bed INFO @ Tue, 02 Aug 2022 10:52:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (679 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:52:40: 5000000 INFO @ Tue, 02 Aug 2022 10:52:46: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:52:52: 7000000 INFO @ Tue, 02 Aug 2022 10:52:53: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:52:58: 8000000 INFO @ Tue, 02 Aug 2022 10:53:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110321/SRX13110321.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:53:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110321/SRX13110321.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:53:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110321/SRX13110321.10_summits.bed INFO @ Tue, 02 Aug 2022 10:53:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (379 records, 4 fields): 49 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:53:03: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:53:03: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:53:03: #1 total tags in treatment: 8710690 INFO @ Tue, 02 Aug 2022 10:53:03: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:53:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:53:03: #1 tags after filtering in treatment: 8710690 INFO @ Tue, 02 Aug 2022 10:53:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:53:03: #1 finished! INFO @ Tue, 02 Aug 2022 10:53:03: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:53:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:53:03: #2 number of paired peaks: 308 WARNING @ Tue, 02 Aug 2022 10:53:03: Fewer paired peaks (308) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 308 pairs to build model! INFO @ Tue, 02 Aug 2022 10:53:03: start model_add_line... INFO @ Tue, 02 Aug 2022 10:53:04: start X-correlation... INFO @ Tue, 02 Aug 2022 10:53:04: end of X-cor INFO @ Tue, 02 Aug 2022 10:53:04: #2 finished! INFO @ Tue, 02 Aug 2022 10:53:04: #2 predicted fragment length is 74 bps INFO @ Tue, 02 Aug 2022 10:53:04: #2 alternative fragment length(s) may be 4,74,562,598 bps INFO @ Tue, 02 Aug 2022 10:53:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110321/SRX13110321.20_model.r WARNING @ Tue, 02 Aug 2022 10:53:04: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:53:04: #2 You may need to consider one of the other alternative d(s): 4,74,562,598 WARNING @ Tue, 02 Aug 2022 10:53:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:53:04: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:53:04: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:53:21: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:53:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110321/SRX13110321.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:53:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110321/SRX13110321.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:53:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110321/SRX13110321.20_summits.bed INFO @ Tue, 02 Aug 2022 10:53:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (206 records, 4 fields): 96 millis CompletedMACS2peakCalling