Job ID = 16434898 SRX = SRX11633391 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 9789573 spots for SRR15329099/SRR15329099.sra Written 9789573 spots for SRR15329099/SRR15329099.sra fastq に変換しました。 bowtie でマッピング中... Your job 16434971 ("srTce11") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:34 9789573 reads; of these: 9789573 (100.00%) were unpaired; of these: 542960 (5.55%) aligned 0 times 7927538 (80.98%) aligned exactly 1 time 1319075 (13.47%) aligned >1 times 94.45% overall alignment rate Time searching: 00:03:35 Overall time: 00:03:35 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] 515489 / 9246613 = 0.0557 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 10:22:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX11633391/SRX11633391.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX11633391/SRX11633391.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX11633391/SRX11633391.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX11633391/SRX11633391.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 10:22:34: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:22:34: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:22:45: 1000000 INFO @ Tue, 02 Aug 2022 10:22:55: 2000000 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 10:23:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX11633391/SRX11633391.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX11633391/SRX11633391.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX11633391/SRX11633391.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX11633391/SRX11633391.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 10:23:04: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:23:04: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:23:06: 3000000 INFO @ Tue, 02 Aug 2022 10:23:15: 1000000 INFO @ Tue, 02 Aug 2022 10:23:18: 4000000 INFO @ Tue, 02 Aug 2022 10:23:26: 2000000 INFO @ Tue, 02 Aug 2022 10:23:29: 5000000 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 10:23:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX11633391/SRX11633391.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX11633391/SRX11633391.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX11633391/SRX11633391.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX11633391/SRX11633391.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 10:23:34: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:23:34: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:23:38: 3000000 INFO @ Tue, 02 Aug 2022 10:23:40: 6000000 INFO @ Tue, 02 Aug 2022 10:23:45: 1000000 INFO @ Tue, 02 Aug 2022 10:23:49: 4000000 INFO @ Tue, 02 Aug 2022 10:23:52: 7000000 INFO @ Tue, 02 Aug 2022 10:23:57: 2000000 INFO @ Tue, 02 Aug 2022 10:24:00: 5000000 INFO @ Tue, 02 Aug 2022 10:24:03: 8000000 INFO @ Tue, 02 Aug 2022 10:24:08: 3000000 INFO @ Tue, 02 Aug 2022 10:24:11: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:24:11: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:24:11: #1 total tags in treatment: 8731124 INFO @ Tue, 02 Aug 2022 10:24:11: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:24:11: #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 10:24:11: #1 tags after filtering in treatment: 8731124 INFO @ Tue, 02 Aug 2022 10:24:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:24:11: #1 finished! INFO @ Tue, 02 Aug 2022 10:24:11: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:24:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:24:11: 6000000 INFO @ Tue, 02 Aug 2022 10:24:12: #2 number of paired peaks: 263 WARNING @ Tue, 02 Aug 2022 10:24:12: Fewer paired peaks (263) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 263 pairs to build model! INFO @ Tue, 02 Aug 2022 10:24:12: start model_add_line... INFO @ Tue, 02 Aug 2022 10:24:12: start X-correlation... INFO @ Tue, 02 Aug 2022 10:24:12: end of X-cor INFO @ Tue, 02 Aug 2022 10:24:12: #2 finished! INFO @ Tue, 02 Aug 2022 10:24:12: #2 predicted fragment length is 61 bps INFO @ Tue, 02 Aug 2022 10:24:12: #2 alternative fragment length(s) may be 4,61 bps INFO @ Tue, 02 Aug 2022 10:24:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX11633391/SRX11633391.05_model.r WARNING @ Tue, 02 Aug 2022 10:24:12: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:24:12: #2 You may need to consider one of the other alternative d(s): 4,61 WARNING @ Tue, 02 Aug 2022 10:24:12: #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 10:24:12: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:24:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:24:19: 4000000 INFO @ Tue, 02 Aug 2022 10:24:22: 7000000 INFO @ Tue, 02 Aug 2022 10:24:28: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:24:29: 5000000 INFO @ Tue, 02 Aug 2022 10:24:32: 8000000 INFO @ Tue, 02 Aug 2022 10:24:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX11633391/SRX11633391.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:24:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX11633391/SRX11633391.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:24:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX11633391/SRX11633391.05_summits.bed INFO @ Tue, 02 Aug 2022 10:24:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (437 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:24:40: 6000000 INFO @ Tue, 02 Aug 2022 10:24:40: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:24:40: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:24:40: #1 total tags in treatment: 8731124 INFO @ Tue, 02 Aug 2022 10:24:40: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:24:40: #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 10:24:40: #1 tags after filtering in treatment: 8731124 INFO @ Tue, 02 Aug 2022 10:24:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:24:40: #1 finished! INFO @ Tue, 02 Aug 2022 10:24:40: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:24:40: #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 10:24:41: #2 number of paired peaks: 263 WARNING @ Tue, 02 Aug 2022 10:24:41: Fewer paired peaks (263) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 263 pairs to build model! INFO @ Tue, 02 Aug 2022 10:24:41: start model_add_line... INFO @ Tue, 02 Aug 2022 10:24:41: start X-correlation... INFO @ Tue, 02 Aug 2022 10:24:41: end of X-cor INFO @ Tue, 02 Aug 2022 10:24:41: #2 finished! INFO @ Tue, 02 Aug 2022 10:24:41: #2 predicted fragment length is 61 bps INFO @ Tue, 02 Aug 2022 10:24:41: #2 alternative fragment length(s) may be 4,61 bps INFO @ Tue, 02 Aug 2022 10:24:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX11633391/SRX11633391.10_model.r WARNING @ Tue, 02 Aug 2022 10:24:41: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:24:41: #2 You may need to consider one of the other alternative d(s): 4,61 WARNING @ Tue, 02 Aug 2022 10:24:41: #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 10:24:41: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:24:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:24:50: 7000000 INFO @ Tue, 02 Aug 2022 10:24:57: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:25:01: 8000000 INFO @ Tue, 02 Aug 2022 10:25:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX11633391/SRX11633391.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:25:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX11633391/SRX11633391.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:25:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX11633391/SRX11633391.10_summits.bed INFO @ Tue, 02 Aug 2022 10:25:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (295 records, 4 fields): 26 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:25:09: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:25:09: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:25:09: #1 total tags in treatment: 8731124 INFO @ Tue, 02 Aug 2022 10:25:09: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:25:09: #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 10:25:09: #1 tags after filtering in treatment: 8731124 INFO @ Tue, 02 Aug 2022 10:25:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:25:09: #1 finished! INFO @ Tue, 02 Aug 2022 10:25:09: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:25:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:25:10: #2 number of paired peaks: 263 WARNING @ Tue, 02 Aug 2022 10:25:10: Fewer paired peaks (263) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 263 pairs to build model! INFO @ Tue, 02 Aug 2022 10:25:10: start model_add_line... INFO @ Tue, 02 Aug 2022 10:25:10: start X-correlation... INFO @ Tue, 02 Aug 2022 10:25:10: end of X-cor INFO @ Tue, 02 Aug 2022 10:25:10: #2 finished! INFO @ Tue, 02 Aug 2022 10:25:10: #2 predicted fragment length is 61 bps INFO @ Tue, 02 Aug 2022 10:25:10: #2 alternative fragment length(s) may be 4,61 bps INFO @ Tue, 02 Aug 2022 10:25:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX11633391/SRX11633391.20_model.r WARNING @ Tue, 02 Aug 2022 10:25:10: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:25:10: #2 You may need to consider one of the other alternative d(s): 4,61 WARNING @ Tue, 02 Aug 2022 10:25:10: #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 10:25:10: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:25:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:25:26: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:25:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX11633391/SRX11633391.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:25:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX11633391/SRX11633391.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:25:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX11633391/SRX11633391.20_summits.bed INFO @ Tue, 02 Aug 2022 10:25:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (160 records, 4 fields): 25 millis CompletedMACS2peakCalling