Job ID = 16434836 SRX = SRX10435510 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 22508594 spots for SRR14060942/SRR14060942.sra Written 22508594 spots for SRR14060942/SRR14060942.sra fastq に変換しました。 bowtie でマッピング中... Your job 16434887 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:44 22508594 reads; of these: 22508594 (100.00%) were unpaired; of these: 4680179 (20.79%) aligned 0 times 14858498 (66.01%) aligned exactly 1 time 2969917 (13.19%) aligned >1 times 79.21% overall alignment rate Time searching: 00:06:45 Overall time: 00:06:45 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] 2892977 / 17828415 = 0.1623 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 10:10:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435510/SRX10435510.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435510/SRX10435510.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435510/SRX10435510.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435510/SRX10435510.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 10:10:30: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:10:30: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:10:37: 1000000 INFO @ Tue, 02 Aug 2022 10:10:44: 2000000 INFO @ Tue, 02 Aug 2022 10:10:50: 3000000 INFO @ Tue, 02 Aug 2022 10:10:56: 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 10:11:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435510/SRX10435510.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435510/SRX10435510.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435510/SRX10435510.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435510/SRX10435510.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 10:11:00: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:11:00: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:11:02: 5000000 INFO @ Tue, 02 Aug 2022 10:11:07: 1000000 INFO @ Tue, 02 Aug 2022 10:11:09: 6000000 INFO @ Tue, 02 Aug 2022 10:11:13: 2000000 INFO @ Tue, 02 Aug 2022 10:11:15: 7000000 INFO @ Tue, 02 Aug 2022 10:11:19: 3000000 INFO @ Tue, 02 Aug 2022 10:11:22: 8000000 INFO @ Tue, 02 Aug 2022 10:11:25: 4000000 INFO @ Tue, 02 Aug 2022 10:11:28: 9000000 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 10:11:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435510/SRX10435510.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435510/SRX10435510.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435510/SRX10435510.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435510/SRX10435510.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 10:11:30: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:11:30: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:11:31: 5000000 INFO @ Tue, 02 Aug 2022 10:11:34: 10000000 INFO @ Tue, 02 Aug 2022 10:11:37: 1000000 INFO @ Tue, 02 Aug 2022 10:11:38: 6000000 INFO @ Tue, 02 Aug 2022 10:11:41: 11000000 INFO @ Tue, 02 Aug 2022 10:11:45: 7000000 INFO @ Tue, 02 Aug 2022 10:11:45: 2000000 INFO @ Tue, 02 Aug 2022 10:11:47: 12000000 INFO @ Tue, 02 Aug 2022 10:11:51: 8000000 INFO @ Tue, 02 Aug 2022 10:11:52: 3000000 INFO @ Tue, 02 Aug 2022 10:11:54: 13000000 INFO @ Tue, 02 Aug 2022 10:11:58: 9000000 INFO @ Tue, 02 Aug 2022 10:12:00: 4000000 INFO @ Tue, 02 Aug 2022 10:12:00: 14000000 INFO @ Tue, 02 Aug 2022 10:12:04: 10000000 INFO @ Tue, 02 Aug 2022 10:12:07: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:12:07: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:12:07: #1 total tags in treatment: 14935438 INFO @ Tue, 02 Aug 2022 10:12:07: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:12:07: #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 10:12:07: #1 tags after filtering in treatment: 14935438 INFO @ Tue, 02 Aug 2022 10:12:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:12:07: #1 finished! INFO @ Tue, 02 Aug 2022 10:12:07: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:12:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:12:07: 5000000 INFO @ Tue, 02 Aug 2022 10:12:08: #2 number of paired peaks: 380 WARNING @ Tue, 02 Aug 2022 10:12:08: Fewer paired peaks (380) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 380 pairs to build model! INFO @ Tue, 02 Aug 2022 10:12:08: start model_add_line... INFO @ Tue, 02 Aug 2022 10:12:08: start X-correlation... INFO @ Tue, 02 Aug 2022 10:12:08: end of X-cor INFO @ Tue, 02 Aug 2022 10:12:08: #2 finished! INFO @ Tue, 02 Aug 2022 10:12:08: #2 predicted fragment length is 92 bps INFO @ Tue, 02 Aug 2022 10:12:08: #2 alternative fragment length(s) may be 4,92 bps INFO @ Tue, 02 Aug 2022 10:12:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435510/SRX10435510.05_model.r WARNING @ Tue, 02 Aug 2022 10:12:08: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:12:08: #2 You may need to consider one of the other alternative d(s): 4,92 WARNING @ Tue, 02 Aug 2022 10:12:08: #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 10:12:08: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:12:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:12:11: 11000000 INFO @ Tue, 02 Aug 2022 10:12:14: 6000000 INFO @ Tue, 02 Aug 2022 10:12:17: 12000000 INFO @ Tue, 02 Aug 2022 10:12:21: 7000000 INFO @ Tue, 02 Aug 2022 10:12:24: 13000000 INFO @ Tue, 02 Aug 2022 10:12:28: 8000000 INFO @ Tue, 02 Aug 2022 10:12:30: 14000000 INFO @ Tue, 02 Aug 2022 10:12:35: 9000000 INFO @ Tue, 02 Aug 2022 10:12:36: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:12:36: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:12:36: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:12:36: #1 total tags in treatment: 14935438 INFO @ Tue, 02 Aug 2022 10:12:36: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:12:36: #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 10:12:37: #1 tags after filtering in treatment: 14935438 INFO @ Tue, 02 Aug 2022 10:12:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:12:37: #1 finished! INFO @ Tue, 02 Aug 2022 10:12:37: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:12:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:12:38: #2 number of paired peaks: 380 WARNING @ Tue, 02 Aug 2022 10:12:38: Fewer paired peaks (380) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 380 pairs to build model! INFO @ Tue, 02 Aug 2022 10:12:38: start model_add_line... INFO @ Tue, 02 Aug 2022 10:12:38: start X-correlation... INFO @ Tue, 02 Aug 2022 10:12:38: end of X-cor INFO @ Tue, 02 Aug 2022 10:12:38: #2 finished! INFO @ Tue, 02 Aug 2022 10:12:38: #2 predicted fragment length is 92 bps INFO @ Tue, 02 Aug 2022 10:12:38: #2 alternative fragment length(s) may be 4,92 bps INFO @ Tue, 02 Aug 2022 10:12:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435510/SRX10435510.10_model.r WARNING @ Tue, 02 Aug 2022 10:12:38: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:12:38: #2 You may need to consider one of the other alternative d(s): 4,92 WARNING @ Tue, 02 Aug 2022 10:12:38: #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 10:12:38: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:12:38: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:12:42: 10000000 INFO @ Tue, 02 Aug 2022 10:12:48: 11000000 INFO @ Tue, 02 Aug 2022 10:12:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435510/SRX10435510.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:12:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435510/SRX10435510.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:12:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435510/SRX10435510.05_summits.bed INFO @ Tue, 02 Aug 2022 10:12:50: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1636 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:12:55: 12000000 INFO @ Tue, 02 Aug 2022 10:13:02: 13000000 INFO @ Tue, 02 Aug 2022 10:13:05: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:13:08: 14000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:13:15: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:13:15: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:13:15: #1 total tags in treatment: 14935438 INFO @ Tue, 02 Aug 2022 10:13:15: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:13:15: #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 10:13:15: #1 tags after filtering in treatment: 14935438 INFO @ Tue, 02 Aug 2022 10:13:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:13:15: #1 finished! INFO @ Tue, 02 Aug 2022 10:13:15: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:13:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:13:16: #2 number of paired peaks: 380 WARNING @ Tue, 02 Aug 2022 10:13:16: Fewer paired peaks (380) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 380 pairs to build model! INFO @ Tue, 02 Aug 2022 10:13:16: start model_add_line... INFO @ Tue, 02 Aug 2022 10:13:16: start X-correlation... INFO @ Tue, 02 Aug 2022 10:13:16: end of X-cor INFO @ Tue, 02 Aug 2022 10:13:16: #2 finished! INFO @ Tue, 02 Aug 2022 10:13:16: #2 predicted fragment length is 92 bps INFO @ Tue, 02 Aug 2022 10:13:16: #2 alternative fragment length(s) may be 4,92 bps INFO @ Tue, 02 Aug 2022 10:13:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435510/SRX10435510.20_model.r WARNING @ Tue, 02 Aug 2022 10:13:16: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:13:16: #2 You may need to consider one of the other alternative d(s): 4,92 WARNING @ Tue, 02 Aug 2022 10:13:16: #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 10:13:16: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:13:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:13:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435510/SRX10435510.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:13:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435510/SRX10435510.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:13:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435510/SRX10435510.10_summits.bed INFO @ Tue, 02 Aug 2022 10:13:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1081 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:13:43: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:13:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435510/SRX10435510.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:13:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435510/SRX10435510.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:13:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435510/SRX10435510.20_summits.bed INFO @ Tue, 02 Aug 2022 10:13:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (595 records, 4 fields): 25 millis CompletedMACS2peakCalling