Job ID = 14158083 SRX = SRX10040012 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: 00:04:16 22508207 reads; of these: 22508207 (100.00%) were unpaired; of these: 1513057 (6.72%) aligned 0 times 16001548 (71.09%) aligned exactly 1 time 4993602 (22.19%) aligned >1 times 93.28% overall alignment rate Time searching: 00:04:16 Overall time: 00:04:16 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] 3274049 / 20995150 = 0.1559 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 14:26:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10040012/SRX10040012.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10040012/SRX10040012.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10040012/SRX10040012.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10040012/SRX10040012.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 @ Wed, 08 Dec 2021 14:26:16: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:26:16: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:26:21: 1000000 INFO @ Wed, 08 Dec 2021 14:26:25: 2000000 INFO @ Wed, 08 Dec 2021 14:26:30: 3000000 INFO @ Wed, 08 Dec 2021 14:26:34: 4000000 INFO @ Wed, 08 Dec 2021 14:26:39: 5000000 INFO @ Wed, 08 Dec 2021 14:26:43: 6000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 14:26:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10040012/SRX10040012.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10040012/SRX10040012.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10040012/SRX10040012.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10040012/SRX10040012.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 @ Wed, 08 Dec 2021 14:26:46: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:26:46: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:26:48: 7000000 INFO @ Wed, 08 Dec 2021 14:26:51: 1000000 INFO @ Wed, 08 Dec 2021 14:26:52: 8000000 INFO @ Wed, 08 Dec 2021 14:26:55: 2000000 INFO @ Wed, 08 Dec 2021 14:26:57: 9000000 INFO @ Wed, 08 Dec 2021 14:27:00: 3000000 INFO @ Wed, 08 Dec 2021 14:27:01: 10000000 INFO @ Wed, 08 Dec 2021 14:27:04: 4000000 INFO @ Wed, 08 Dec 2021 14:27:06: 11000000 INFO @ Wed, 08 Dec 2021 14:27:09: 5000000 INFO @ Wed, 08 Dec 2021 14:27:10: 12000000 INFO @ Wed, 08 Dec 2021 14:27:13: 6000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 14:27:15: 13000000 INFO @ Wed, 08 Dec 2021 14:27:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10040012/SRX10040012.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10040012/SRX10040012.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10040012/SRX10040012.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10040012/SRX10040012.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 @ Wed, 08 Dec 2021 14:27:16: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:27:16: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:27:18: 7000000 INFO @ Wed, 08 Dec 2021 14:27:19: 14000000 INFO @ Wed, 08 Dec 2021 14:27:21: 1000000 INFO @ Wed, 08 Dec 2021 14:27:23: 8000000 INFO @ Wed, 08 Dec 2021 14:27:24: 15000000 INFO @ Wed, 08 Dec 2021 14:27:25: 2000000 INFO @ Wed, 08 Dec 2021 14:27:27: 9000000 INFO @ Wed, 08 Dec 2021 14:27:28: 16000000 INFO @ Wed, 08 Dec 2021 14:27:30: 3000000 INFO @ Wed, 08 Dec 2021 14:27:32: 10000000 INFO @ Wed, 08 Dec 2021 14:27:33: 17000000 INFO @ Wed, 08 Dec 2021 14:27:35: 4000000 INFO @ Wed, 08 Dec 2021 14:27:36: 11000000 INFO @ Wed, 08 Dec 2021 14:27:36: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 14:27:36: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 14:27:36: #1 total tags in treatment: 17721101 INFO @ Wed, 08 Dec 2021 14:27:36: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:27:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 14:27:36: #1 tags after filtering in treatment: 17721101 INFO @ Wed, 08 Dec 2021 14:27:36: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:27:36: #1 finished! INFO @ Wed, 08 Dec 2021 14:27:36: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:27:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:27:38: #2 number of paired peaks: 346 WARNING @ Wed, 08 Dec 2021 14:27:38: Fewer paired peaks (346) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 346 pairs to build model! INFO @ Wed, 08 Dec 2021 14:27:38: start model_add_line... INFO @ Wed, 08 Dec 2021 14:27:38: start X-correlation... INFO @ Wed, 08 Dec 2021 14:27:38: end of X-cor INFO @ Wed, 08 Dec 2021 14:27:38: #2 finished! INFO @ Wed, 08 Dec 2021 14:27:38: #2 predicted fragment length is 48 bps INFO @ Wed, 08 Dec 2021 14:27:38: #2 alternative fragment length(s) may be 1,38,48 bps INFO @ Wed, 08 Dec 2021 14:27:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10040012/SRX10040012.05_model.r WARNING @ Wed, 08 Dec 2021 14:27:38: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:27:38: #2 You may need to consider one of the other alternative d(s): 1,38,48 WARNING @ Wed, 08 Dec 2021 14:27:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 14:27:38: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:27:38: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:27:39: 5000000 INFO @ Wed, 08 Dec 2021 14:27:41: 12000000 INFO @ Wed, 08 Dec 2021 14:27:44: 6000000 INFO @ Wed, 08 Dec 2021 14:27:45: 13000000 INFO @ Wed, 08 Dec 2021 14:27:48: 7000000 INFO @ Wed, 08 Dec 2021 14:27:50: 14000000 INFO @ Wed, 08 Dec 2021 14:27:53: 8000000 INFO @ Wed, 08 Dec 2021 14:27:54: 15000000 INFO @ Wed, 08 Dec 2021 14:27:57: 9000000 INFO @ Wed, 08 Dec 2021 14:27:58: 16000000 INFO @ Wed, 08 Dec 2021 14:28:02: 10000000 INFO @ Wed, 08 Dec 2021 14:28:03: 17000000 INFO @ Wed, 08 Dec 2021 14:28:05: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:28:06: 11000000 INFO @ Wed, 08 Dec 2021 14:28:06: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 14:28:06: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 14:28:06: #1 total tags in treatment: 17721101 INFO @ Wed, 08 Dec 2021 14:28:06: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:28:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 14:28:07: #1 tags after filtering in treatment: 17721101 INFO @ Wed, 08 Dec 2021 14:28:07: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:28:07: #1 finished! INFO @ Wed, 08 Dec 2021 14:28:07: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:28:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:28:08: #2 number of paired peaks: 346 WARNING @ Wed, 08 Dec 2021 14:28:08: Fewer paired peaks (346) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 346 pairs to build model! INFO @ Wed, 08 Dec 2021 14:28:08: start model_add_line... INFO @ Wed, 08 Dec 2021 14:28:08: start X-correlation... INFO @ Wed, 08 Dec 2021 14:28:08: end of X-cor INFO @ Wed, 08 Dec 2021 14:28:08: #2 finished! INFO @ Wed, 08 Dec 2021 14:28:08: #2 predicted fragment length is 48 bps INFO @ Wed, 08 Dec 2021 14:28:08: #2 alternative fragment length(s) may be 1,38,48 bps INFO @ Wed, 08 Dec 2021 14:28:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10040012/SRX10040012.10_model.r WARNING @ Wed, 08 Dec 2021 14:28:08: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:28:08: #2 You may need to consider one of the other alternative d(s): 1,38,48 WARNING @ Wed, 08 Dec 2021 14:28:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 14:28:08: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:28:08: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:28:10: 12000000 INFO @ Wed, 08 Dec 2021 14:28:15: 13000000 INFO @ Wed, 08 Dec 2021 14:28:19: 14000000 INFO @ Wed, 08 Dec 2021 14:28:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10040012/SRX10040012.05_peaks.xls INFO @ Wed, 08 Dec 2021 14:28:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10040012/SRX10040012.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:28:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10040012/SRX10040012.05_summits.bed INFO @ Wed, 08 Dec 2021 14:28:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1172 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:28:24: 15000000 INFO @ Wed, 08 Dec 2021 14:28:28: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 14:28:33: 17000000 INFO @ Wed, 08 Dec 2021 14:28:36: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 14:28:36: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 14:28:36: #1 total tags in treatment: 17721101 INFO @ Wed, 08 Dec 2021 14:28:36: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:28:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 14:28:36: #1 tags after filtering in treatment: 17721101 INFO @ Wed, 08 Dec 2021 14:28:36: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:28:36: #1 finished! INFO @ Wed, 08 Dec 2021 14:28:36: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:28:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:28:37: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:28:37: #2 number of paired peaks: 346 WARNING @ Wed, 08 Dec 2021 14:28:37: Fewer paired peaks (346) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 346 pairs to build model! INFO @ Wed, 08 Dec 2021 14:28:37: start model_add_line... INFO @ Wed, 08 Dec 2021 14:28:37: start X-correlation... INFO @ Wed, 08 Dec 2021 14:28:37: end of X-cor INFO @ Wed, 08 Dec 2021 14:28:37: #2 finished! INFO @ Wed, 08 Dec 2021 14:28:37: #2 predicted fragment length is 48 bps INFO @ Wed, 08 Dec 2021 14:28:37: #2 alternative fragment length(s) may be 1,38,48 bps INFO @ Wed, 08 Dec 2021 14:28:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10040012/SRX10040012.20_model.r WARNING @ Wed, 08 Dec 2021 14:28:37: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:28:37: #2 You may need to consider one of the other alternative d(s): 1,38,48 WARNING @ Wed, 08 Dec 2021 14:28:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 14:28:37: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:28:37: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:28:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10040012/SRX10040012.10_peaks.xls INFO @ Wed, 08 Dec 2021 14:28:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10040012/SRX10040012.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:28:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10040012/SRX10040012.10_summits.bed INFO @ Wed, 08 Dec 2021 14:28:51: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (448 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:29:05: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 14:29:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10040012/SRX10040012.20_peaks.xls INFO @ Wed, 08 Dec 2021 14:29:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10040012/SRX10040012.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:29:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10040012/SRX10040012.20_summits.bed INFO @ Wed, 08 Dec 2021 14:29:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (156 records, 4 fields): 1 millis CompletedMACS2peakCalling