Job ID = 16436161 SRX = SRX13110375 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: 00:04:08 14042144 reads; of these: 14042144 (100.00%) were unpaired; of these: 1435070 (10.22%) aligned 0 times 10821271 (77.06%) aligned exactly 1 time 1785803 (12.72%) aligned >1 times 89.78% overall alignment rate Time searching: 00:04:08 Overall time: 00:04:08 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 8 files... [bam_rmdupse_core] 2177825 / 12607074 = 0.1727 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 11:07:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110375/SRX13110375.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110375/SRX13110375.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110375/SRX13110375.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110375/SRX13110375.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 11:07:40: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:07:40: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:07:46: 1000000 INFO @ Tue, 02 Aug 2022 11:07:52: 2000000 INFO @ Tue, 02 Aug 2022 11:07:58: 3000000 INFO @ Tue, 02 Aug 2022 11:08:04: 4000000 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 11:08:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110375/SRX13110375.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110375/SRX13110375.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110375/SRX13110375.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110375/SRX13110375.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 11:08:09: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:08:09: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:08:10: 5000000 INFO @ Tue, 02 Aug 2022 11:08:16: 1000000 INFO @ Tue, 02 Aug 2022 11:08:17: 6000000 INFO @ Tue, 02 Aug 2022 11:08:23: 2000000 INFO @ Tue, 02 Aug 2022 11:08:24: 7000000 INFO @ Tue, 02 Aug 2022 11:08:30: 3000000 INFO @ Tue, 02 Aug 2022 11:08:31: 8000000 INFO @ Tue, 02 Aug 2022 11:08:37: 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 11:08:38: 9000000 INFO @ Tue, 02 Aug 2022 11:08:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110375/SRX13110375.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110375/SRX13110375.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110375/SRX13110375.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110375/SRX13110375.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 11:08:39: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:08:39: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:08:45: 5000000 INFO @ Tue, 02 Aug 2022 11:08:46: 10000000 INFO @ Tue, 02 Aug 2022 11:08:48: 1000000 INFO @ Tue, 02 Aug 2022 11:08:49: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:08:49: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:08:49: #1 total tags in treatment: 10429249 INFO @ Tue, 02 Aug 2022 11:08:49: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:08:49: #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 11:08:49: #1 tags after filtering in treatment: 10429249 INFO @ Tue, 02 Aug 2022 11:08:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:08:49: #1 finished! INFO @ Tue, 02 Aug 2022 11:08:49: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:08:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:08:50: #2 number of paired peaks: 264 WARNING @ Tue, 02 Aug 2022 11:08:50: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Tue, 02 Aug 2022 11:08:50: start model_add_line... INFO @ Tue, 02 Aug 2022 11:08:50: start X-correlation... INFO @ Tue, 02 Aug 2022 11:08:50: end of X-cor INFO @ Tue, 02 Aug 2022 11:08:50: #2 finished! INFO @ Tue, 02 Aug 2022 11:08:50: #2 predicted fragment length is 72 bps INFO @ Tue, 02 Aug 2022 11:08:50: #2 alternative fragment length(s) may be 4,72,563 bps INFO @ Tue, 02 Aug 2022 11:08:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110375/SRX13110375.05_model.r WARNING @ Tue, 02 Aug 2022 11:08:50: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:08:50: #2 You may need to consider one of the other alternative d(s): 4,72,563 WARNING @ Tue, 02 Aug 2022 11:08:50: #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 11:08:50: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:08:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:08:52: 6000000 INFO @ Tue, 02 Aug 2022 11:08:56: 2000000 INFO @ Tue, 02 Aug 2022 11:09:00: 7000000 INFO @ Tue, 02 Aug 2022 11:09:05: 3000000 INFO @ Tue, 02 Aug 2022 11:09:07: 8000000 INFO @ Tue, 02 Aug 2022 11:09:10: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:09:13: 4000000 INFO @ Tue, 02 Aug 2022 11:09:15: 9000000 INFO @ Tue, 02 Aug 2022 11:09:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110375/SRX13110375.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:09:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110375/SRX13110375.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:09:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110375/SRX13110375.05_summits.bed INFO @ Tue, 02 Aug 2022 11:09:20: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (566 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:09:21: 5000000 INFO @ Tue, 02 Aug 2022 11:09:22: 10000000 INFO @ Tue, 02 Aug 2022 11:09:26: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:09:26: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:09:26: #1 total tags in treatment: 10429249 INFO @ Tue, 02 Aug 2022 11:09:26: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:09:26: #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 11:09:26: #1 tags after filtering in treatment: 10429249 INFO @ Tue, 02 Aug 2022 11:09:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:09:26: #1 finished! INFO @ Tue, 02 Aug 2022 11:09:26: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:09:26: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:09:26: #2 number of paired peaks: 264 WARNING @ Tue, 02 Aug 2022 11:09:26: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Tue, 02 Aug 2022 11:09:26: start model_add_line... INFO @ Tue, 02 Aug 2022 11:09:26: start X-correlation... INFO @ Tue, 02 Aug 2022 11:09:27: end of X-cor INFO @ Tue, 02 Aug 2022 11:09:27: #2 finished! INFO @ Tue, 02 Aug 2022 11:09:27: #2 predicted fragment length is 72 bps INFO @ Tue, 02 Aug 2022 11:09:27: #2 alternative fragment length(s) may be 4,72,563 bps INFO @ Tue, 02 Aug 2022 11:09:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110375/SRX13110375.10_model.r WARNING @ Tue, 02 Aug 2022 11:09:27: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:09:27: #2 You may need to consider one of the other alternative d(s): 4,72,563 WARNING @ Tue, 02 Aug 2022 11:09:27: #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 11:09:27: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:09:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:09:29: 6000000 INFO @ Tue, 02 Aug 2022 11:09:37: 7000000 INFO @ Tue, 02 Aug 2022 11:09:44: 8000000 INFO @ Tue, 02 Aug 2022 11:09:46: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:09:52: 9000000 INFO @ Tue, 02 Aug 2022 11:09:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110375/SRX13110375.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:09:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110375/SRX13110375.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:09:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110375/SRX13110375.10_summits.bed INFO @ Tue, 02 Aug 2022 11:09:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (376 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:10:00: 10000000 INFO @ Tue, 02 Aug 2022 11:10:03: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:10:03: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:10:03: #1 total tags in treatment: 10429249 INFO @ Tue, 02 Aug 2022 11:10:03: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:10:03: #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 11:10:03: #1 tags after filtering in treatment: 10429249 INFO @ Tue, 02 Aug 2022 11:10:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:10:03: #1 finished! INFO @ Tue, 02 Aug 2022 11:10:03: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:10:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:10:04: #2 number of paired peaks: 264 WARNING @ Tue, 02 Aug 2022 11:10:04: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Tue, 02 Aug 2022 11:10:04: start model_add_line... INFO @ Tue, 02 Aug 2022 11:10:04: start X-correlation... INFO @ Tue, 02 Aug 2022 11:10:04: end of X-cor INFO @ Tue, 02 Aug 2022 11:10:04: #2 finished! INFO @ Tue, 02 Aug 2022 11:10:04: #2 predicted fragment length is 72 bps INFO @ Tue, 02 Aug 2022 11:10:04: #2 alternative fragment length(s) may be 4,72,563 bps INFO @ Tue, 02 Aug 2022 11:10:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110375/SRX13110375.20_model.r WARNING @ Tue, 02 Aug 2022 11:10:04: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:10:04: #2 You may need to consider one of the other alternative d(s): 4,72,563 WARNING @ Tue, 02 Aug 2022 11:10:04: #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 11:10:04: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:10:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:10:24: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:10:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110375/SRX13110375.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:10:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110375/SRX13110375.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:10:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110375/SRX13110375.20_summits.bed INFO @ Tue, 02 Aug 2022 11:10:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (202 records, 4 fields): 99 millis CompletedMACS2peakCalling