Job ID = 14159588 SRX = SRX3180775 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 17002312 spots for SRR6030426/SRR6030426.sra Written 17002312 spots for SRR6030426/SRR6030426.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159947 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:11 17002312 reads; of these: 17002312 (100.00%) were unpaired; of these: 544740 (3.20%) aligned 0 times 13711922 (80.65%) aligned exactly 1 time 2745650 (16.15%) aligned >1 times 96.80% overall alignment rate Time searching: 00:04:11 Overall time: 00:04:11 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] 2477586 / 16457572 = 0.1505 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 23:06:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180775/SRX3180775.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180775/SRX3180775.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180775/SRX3180775.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180775/SRX3180775.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 23:06:44: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:06:44: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:06:53: 1000000 INFO @ Wed, 08 Dec 2021 23:07:03: 2000000 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 23:07:13: 3000000 INFO @ Wed, 08 Dec 2021 23:07:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180775/SRX3180775.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180775/SRX3180775.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180775/SRX3180775.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180775/SRX3180775.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 23:07:14: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:07:14: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:07:24: 4000000 INFO @ Wed, 08 Dec 2021 23:07:24: 1000000 INFO @ Wed, 08 Dec 2021 23:07:34: 2000000 INFO @ Wed, 08 Dec 2021 23:07:34: 5000000 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 23:07:44: 3000000 INFO @ Wed, 08 Dec 2021 23:07:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180775/SRX3180775.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180775/SRX3180775.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180775/SRX3180775.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180775/SRX3180775.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 23:07:44: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:07:44: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:07:44: 6000000 INFO @ Wed, 08 Dec 2021 23:07:53: 4000000 INFO @ Wed, 08 Dec 2021 23:07:54: 7000000 INFO @ Wed, 08 Dec 2021 23:07:55: 1000000 INFO @ Wed, 08 Dec 2021 23:08:03: 5000000 INFO @ Wed, 08 Dec 2021 23:08:04: 8000000 INFO @ Wed, 08 Dec 2021 23:08:05: 2000000 INFO @ Wed, 08 Dec 2021 23:08:13: 6000000 INFO @ Wed, 08 Dec 2021 23:08:13: 9000000 INFO @ Wed, 08 Dec 2021 23:08:15: 3000000 INFO @ Wed, 08 Dec 2021 23:08:22: 7000000 INFO @ Wed, 08 Dec 2021 23:08:23: 10000000 INFO @ Wed, 08 Dec 2021 23:08:25: 4000000 INFO @ Wed, 08 Dec 2021 23:08:32: 8000000 INFO @ Wed, 08 Dec 2021 23:08:33: 11000000 INFO @ Wed, 08 Dec 2021 23:08:35: 5000000 INFO @ Wed, 08 Dec 2021 23:08:42: 9000000 INFO @ Wed, 08 Dec 2021 23:08:43: 12000000 INFO @ Wed, 08 Dec 2021 23:08:46: 6000000 INFO @ Wed, 08 Dec 2021 23:08:52: 10000000 INFO @ Wed, 08 Dec 2021 23:08:52: 13000000 INFO @ Wed, 08 Dec 2021 23:08:56: 7000000 INFO @ Wed, 08 Dec 2021 23:09:01: 11000000 INFO @ Wed, 08 Dec 2021 23:09:02: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 23:09:02: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 23:09:02: #1 total tags in treatment: 13979986 INFO @ Wed, 08 Dec 2021 23:09:02: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:09:02: #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 23:09:02: #1 tags after filtering in treatment: 13979986 INFO @ Wed, 08 Dec 2021 23:09:02: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 23:09:02: #1 finished! INFO @ Wed, 08 Dec 2021 23:09:02: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:09:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:09:03: #2 number of paired peaks: 330 WARNING @ Wed, 08 Dec 2021 23:09:03: Fewer paired peaks (330) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 330 pairs to build model! INFO @ Wed, 08 Dec 2021 23:09:03: start model_add_line... INFO @ Wed, 08 Dec 2021 23:09:03: start X-correlation... INFO @ Wed, 08 Dec 2021 23:09:03: end of X-cor INFO @ Wed, 08 Dec 2021 23:09:03: #2 finished! INFO @ Wed, 08 Dec 2021 23:09:03: #2 predicted fragment length is 47 bps INFO @ Wed, 08 Dec 2021 23:09:03: #2 alternative fragment length(s) may be 2,47,577 bps INFO @ Wed, 08 Dec 2021 23:09:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180775/SRX3180775.05_model.r WARNING @ Wed, 08 Dec 2021 23:09:03: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:09:03: #2 You may need to consider one of the other alternative d(s): 2,47,577 WARNING @ Wed, 08 Dec 2021 23:09:03: #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 23:09:03: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:09:03: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:09:07: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 23:09:11: 12000000 INFO @ Wed, 08 Dec 2021 23:09:17: 9000000 INFO @ Wed, 08 Dec 2021 23:09:21: 13000000 INFO @ Wed, 08 Dec 2021 23:09:26: 10000000 INFO @ Wed, 08 Dec 2021 23:09:27: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:09:30: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 23:09:30: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 23:09:30: #1 total tags in treatment: 13979986 INFO @ Wed, 08 Dec 2021 23:09:30: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:09:30: #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 23:09:30: #1 tags after filtering in treatment: 13979986 INFO @ Wed, 08 Dec 2021 23:09:30: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 23:09:30: #1 finished! INFO @ Wed, 08 Dec 2021 23:09:30: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:09:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:09:31: #2 number of paired peaks: 330 WARNING @ Wed, 08 Dec 2021 23:09:31: Fewer paired peaks (330) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 330 pairs to build model! INFO @ Wed, 08 Dec 2021 23:09:31: start model_add_line... INFO @ Wed, 08 Dec 2021 23:09:31: start X-correlation... INFO @ Wed, 08 Dec 2021 23:09:31: end of X-cor INFO @ Wed, 08 Dec 2021 23:09:31: #2 finished! INFO @ Wed, 08 Dec 2021 23:09:31: #2 predicted fragment length is 47 bps INFO @ Wed, 08 Dec 2021 23:09:31: #2 alternative fragment length(s) may be 2,47,577 bps INFO @ Wed, 08 Dec 2021 23:09:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180775/SRX3180775.10_model.r WARNING @ Wed, 08 Dec 2021 23:09:31: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:09:31: #2 You may need to consider one of the other alternative d(s): 2,47,577 WARNING @ Wed, 08 Dec 2021 23:09:31: #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 23:09:31: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:09:31: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:09:36: 11000000 INFO @ Wed, 08 Dec 2021 23:09:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180775/SRX3180775.05_peaks.xls INFO @ Wed, 08 Dec 2021 23:09:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180775/SRX3180775.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:09:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180775/SRX3180775.05_summits.bed INFO @ Wed, 08 Dec 2021 23:09:40: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (717 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 23:09:45: 12000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 23:09:54: 13000000 INFO @ Wed, 08 Dec 2021 23:09:55: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:10:03: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 23:10:03: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 23:10:03: #1 total tags in treatment: 13979986 INFO @ Wed, 08 Dec 2021 23:10:03: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:10:03: #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 23:10:04: #1 tags after filtering in treatment: 13979986 INFO @ Wed, 08 Dec 2021 23:10:04: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 23:10:04: #1 finished! INFO @ Wed, 08 Dec 2021 23:10:04: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:10:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:10:05: #2 number of paired peaks: 330 WARNING @ Wed, 08 Dec 2021 23:10:05: Fewer paired peaks (330) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 330 pairs to build model! INFO @ Wed, 08 Dec 2021 23:10:05: start model_add_line... INFO @ Wed, 08 Dec 2021 23:10:05: start X-correlation... INFO @ Wed, 08 Dec 2021 23:10:05: end of X-cor INFO @ Wed, 08 Dec 2021 23:10:05: #2 finished! INFO @ Wed, 08 Dec 2021 23:10:05: #2 predicted fragment length is 47 bps INFO @ Wed, 08 Dec 2021 23:10:05: #2 alternative fragment length(s) may be 2,47,577 bps INFO @ Wed, 08 Dec 2021 23:10:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180775/SRX3180775.20_model.r WARNING @ Wed, 08 Dec 2021 23:10:05: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:10:05: #2 You may need to consider one of the other alternative d(s): 2,47,577 WARNING @ Wed, 08 Dec 2021 23:10:05: #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 23:10:05: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:10:05: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:10:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180775/SRX3180775.10_peaks.xls INFO @ Wed, 08 Dec 2021 23:10:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180775/SRX3180775.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:10:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180775/SRX3180775.10_summits.bed INFO @ Wed, 08 Dec 2021 23:10:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (459 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 23:10:28: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:10:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180775/SRX3180775.20_peaks.xls INFO @ Wed, 08 Dec 2021 23:10:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180775/SRX3180775.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:10:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180775/SRX3180775.20_summits.bed INFO @ Wed, 08 Dec 2021 23:10:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (189 records, 4 fields): 1 millis CompletedMACS2peakCalling