Job ID = 16434793 SRX = SRX11633400 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 13997378 spots for SRR15329109/SRR15329109.sra Written 13997378 spots for SRR15329109/SRR15329109.sra fastq に変換しました。 bowtie でマッピング中... Your job 16434860 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:04:32 13997378 reads; of these: 13997378 (100.00%) were unpaired; of these: 1672683 (11.95%) aligned 0 times 10560151 (75.44%) aligned exactly 1 time 1764544 (12.61%) aligned >1 times 88.05% overall alignment rate Time searching: 00:04:33 Overall time: 00:04:33 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] 7675611 / 12324695 = 0.6228 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 10:04:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX11633400/SRX11633400.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX11633400/SRX11633400.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX11633400/SRX11633400.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX11633400/SRX11633400.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 10:04:40: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:04:40: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:04:45: 1000000 INFO @ Tue, 02 Aug 2022 10:04:51: 2000000 INFO @ Tue, 02 Aug 2022 10:04:56: 3000000 INFO @ Tue, 02 Aug 2022 10:05:01: 4000000 INFO @ Tue, 02 Aug 2022 10:05:04: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:05:04: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:05:04: #1 total tags in treatment: 4649084 INFO @ Tue, 02 Aug 2022 10:05:04: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:05:04: #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 10:05:05: #1 tags after filtering in treatment: 4649084 INFO @ Tue, 02 Aug 2022 10:05:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:05:05: #1 finished! INFO @ Tue, 02 Aug 2022 10:05:05: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:05:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:05:05: #2 number of paired peaks: 499 WARNING @ Tue, 02 Aug 2022 10:05:05: Fewer paired peaks (499) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 499 pairs to build model! INFO @ Tue, 02 Aug 2022 10:05:05: start model_add_line... INFO @ Tue, 02 Aug 2022 10:05:05: start X-correlation... INFO @ Tue, 02 Aug 2022 10:05:05: end of X-cor INFO @ Tue, 02 Aug 2022 10:05:05: #2 finished! INFO @ Tue, 02 Aug 2022 10:05:05: #2 predicted fragment length is 70 bps INFO @ Tue, 02 Aug 2022 10:05:05: #2 alternative fragment length(s) may be 70 bps INFO @ Tue, 02 Aug 2022 10:05:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX11633400/SRX11633400.05_model.r WARNING @ Tue, 02 Aug 2022 10:05:05: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:05:05: #2 You may need to consider one of the other alternative d(s): 70 WARNING @ Tue, 02 Aug 2022 10:05:05: #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 10:05:05: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:05:05: #3 Pre-compute pvalue-qvalue table... 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 10:05:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX11633400/SRX11633400.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX11633400/SRX11633400.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX11633400/SRX11633400.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX11633400/SRX11633400.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 10:05:09: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:05:09: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:05:15: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:05:15: 1000000 INFO @ Tue, 02 Aug 2022 10:05:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX11633400/SRX11633400.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:05:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX11633400/SRX11633400.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:05:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX11633400/SRX11633400.05_summits.bed INFO @ Tue, 02 Aug 2022 10:05:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (517 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:05:22: 2000000 INFO @ Tue, 02 Aug 2022 10:05:28: 3000000 INFO @ Tue, 02 Aug 2022 10:05:35: 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 10:05:39: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:05:39: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:05:39: #1 total tags in treatment: 4649084 INFO @ Tue, 02 Aug 2022 10:05:39: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:05:39: #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 10:05:39: #1 tags after filtering in treatment: 4649084 INFO @ Tue, 02 Aug 2022 10:05:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:05:39: #1 finished! INFO @ Tue, 02 Aug 2022 10:05:39: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:05:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:05:39: #2 number of paired peaks: 499 WARNING @ Tue, 02 Aug 2022 10:05:39: Fewer paired peaks (499) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 499 pairs to build model! INFO @ Tue, 02 Aug 2022 10:05:39: start model_add_line... INFO @ Tue, 02 Aug 2022 10:05:39: start X-correlation... INFO @ Tue, 02 Aug 2022 10:05:39: end of X-cor INFO @ Tue, 02 Aug 2022 10:05:39: #2 finished! INFO @ Tue, 02 Aug 2022 10:05:39: #2 predicted fragment length is 70 bps INFO @ Tue, 02 Aug 2022 10:05:39: #2 alternative fragment length(s) may be 70 bps INFO @ Tue, 02 Aug 2022 10:05:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX11633400/SRX11633400.10_model.r WARNING @ Tue, 02 Aug 2022 10:05:39: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:05:39: #2 You may need to consider one of the other alternative d(s): 70 WARNING @ Tue, 02 Aug 2022 10:05:39: #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 10:05:39: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:05:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:05:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX11633400/SRX11633400.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX11633400/SRX11633400.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX11633400/SRX11633400.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX11633400/SRX11633400.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 10:05:39: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:05:39: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:05:45: 1000000 INFO @ Tue, 02 Aug 2022 10:05:49: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:05:51: 2000000 INFO @ Tue, 02 Aug 2022 10:05:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX11633400/SRX11633400.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:05:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX11633400/SRX11633400.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:05:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX11633400/SRX11633400.10_summits.bed INFO @ Tue, 02 Aug 2022 10:05:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (310 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:05:56: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:06:02: 4000000 INFO @ Tue, 02 Aug 2022 10:06:06: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:06:06: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:06:06: #1 total tags in treatment: 4649084 INFO @ Tue, 02 Aug 2022 10:06:06: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:06:06: #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 10:06:06: #1 tags after filtering in treatment: 4649084 INFO @ Tue, 02 Aug 2022 10:06:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:06:06: #1 finished! INFO @ Tue, 02 Aug 2022 10:06:06: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:06:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:06:06: #2 number of paired peaks: 499 WARNING @ Tue, 02 Aug 2022 10:06:06: Fewer paired peaks (499) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 499 pairs to build model! INFO @ Tue, 02 Aug 2022 10:06:06: start model_add_line... INFO @ Tue, 02 Aug 2022 10:06:06: start X-correlation... INFO @ Tue, 02 Aug 2022 10:06:06: end of X-cor INFO @ Tue, 02 Aug 2022 10:06:06: #2 finished! INFO @ Tue, 02 Aug 2022 10:06:06: #2 predicted fragment length is 70 bps INFO @ Tue, 02 Aug 2022 10:06:06: #2 alternative fragment length(s) may be 70 bps INFO @ Tue, 02 Aug 2022 10:06:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX11633400/SRX11633400.20_model.r WARNING @ Tue, 02 Aug 2022 10:06:06: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:06:06: #2 You may need to consider one of the other alternative d(s): 70 WARNING @ Tue, 02 Aug 2022 10:06:06: #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 10:06:06: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:06:06: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:06:17: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:06:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX11633400/SRX11633400.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:06:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX11633400/SRX11633400.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:06:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX11633400/SRX11633400.20_summits.bed INFO @ Tue, 02 Aug 2022 10:06:22: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (165 records, 4 fields): 16 millis CompletedMACS2peakCalling