Job ID = 6626394 SRX = SRX7262229 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 2849153 spots for SRR10581852/SRR10581852.sra Written 2849153 spots for SRR10581852/SRR10581852.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626429 ("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: 00:00:28 2849153 reads; of these: 2849153 (100.00%) were unpaired; of these: 867131 (30.43%) aligned 0 times 1567815 (55.03%) aligned exactly 1 time 414207 (14.54%) aligned >1 times 69.57% overall alignment rate Time searching: 00:00:28 Overall time: 00:00:28 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] 837320 / 1982022 = 0.4225 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 06:58:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262229/SRX7262229.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262229/SRX7262229.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262229/SRX7262229.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262229/SRX7262229.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, 14 Jul 2020 06:58:58: #1 read tag files... INFO @ Tue, 14 Jul 2020 06:58:58: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 06:59:04: 1000000 INFO @ Tue, 14 Jul 2020 06:59:05: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 06:59:05: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 06:59:05: #1 total tags in treatment: 1144702 INFO @ Tue, 14 Jul 2020 06:59:05: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 06:59:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 06:59:05: #1 tags after filtering in treatment: 1144702 INFO @ Tue, 14 Jul 2020 06:59:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 06:59:05: #1 finished! INFO @ Tue, 14 Jul 2020 06:59:05: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 06:59:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 06:59:05: #2 number of paired peaks: 573 WARNING @ Tue, 14 Jul 2020 06:59:05: Fewer paired peaks (573) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 573 pairs to build model! INFO @ Tue, 14 Jul 2020 06:59:05: start model_add_line... INFO @ Tue, 14 Jul 2020 06:59:05: start X-correlation... INFO @ Tue, 14 Jul 2020 06:59:05: end of X-cor INFO @ Tue, 14 Jul 2020 06:59:05: #2 finished! INFO @ Tue, 14 Jul 2020 06:59:05: #2 predicted fragment length is 50 bps INFO @ Tue, 14 Jul 2020 06:59:05: #2 alternative fragment length(s) may be 50,200,453,532 bps INFO @ Tue, 14 Jul 2020 06:59:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262229/SRX7262229.05_model.r WARNING @ Tue, 14 Jul 2020 06:59:05: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 06:59:05: #2 You may need to consider one of the other alternative d(s): 50,200,453,532 WARNING @ Tue, 14 Jul 2020 06:59:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 06:59:05: #3 Call peaks... INFO @ Tue, 14 Jul 2020 06:59:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 06:59:07: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 06:59:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262229/SRX7262229.05_peaks.xls INFO @ Tue, 14 Jul 2020 06:59:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262229/SRX7262229.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 06:59:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262229/SRX7262229.05_summits.bed INFO @ Tue, 14 Jul 2020 06:59:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (415 records, 4 fields): 15 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 06:59:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262229/SRX7262229.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262229/SRX7262229.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262229/SRX7262229.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262229/SRX7262229.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, 14 Jul 2020 06:59:28: #1 read tag files... INFO @ Tue, 14 Jul 2020 06:59:28: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 06:59:33: 1000000 INFO @ Tue, 14 Jul 2020 06:59:34: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 06:59:34: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 06:59:34: #1 total tags in treatment: 1144702 INFO @ Tue, 14 Jul 2020 06:59:34: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 06:59:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 06:59:34: #1 tags after filtering in treatment: 1144702 INFO @ Tue, 14 Jul 2020 06:59:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 06:59:34: #1 finished! INFO @ Tue, 14 Jul 2020 06:59:34: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 06:59:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 06:59:34: #2 number of paired peaks: 573 WARNING @ Tue, 14 Jul 2020 06:59:34: Fewer paired peaks (573) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 573 pairs to build model! INFO @ Tue, 14 Jul 2020 06:59:34: start model_add_line... INFO @ Tue, 14 Jul 2020 06:59:34: start X-correlation... INFO @ Tue, 14 Jul 2020 06:59:34: end of X-cor INFO @ Tue, 14 Jul 2020 06:59:34: #2 finished! INFO @ Tue, 14 Jul 2020 06:59:34: #2 predicted fragment length is 50 bps INFO @ Tue, 14 Jul 2020 06:59:34: #2 alternative fragment length(s) may be 50,200,453,532 bps INFO @ Tue, 14 Jul 2020 06:59:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262229/SRX7262229.10_model.r WARNING @ Tue, 14 Jul 2020 06:59:34: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 06:59:34: #2 You may need to consider one of the other alternative d(s): 50,200,453,532 WARNING @ Tue, 14 Jul 2020 06:59:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 06:59:34: #3 Call peaks... INFO @ Tue, 14 Jul 2020 06:59:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 06:59:37: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 06:59:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262229/SRX7262229.10_peaks.xls INFO @ Tue, 14 Jul 2020 06:59:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262229/SRX7262229.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 06:59:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262229/SRX7262229.10_summits.bed INFO @ Tue, 14 Jul 2020 06:59:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (221 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 06:59:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262229/SRX7262229.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262229/SRX7262229.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262229/SRX7262229.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262229/SRX7262229.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, 14 Jul 2020 06:59:58: #1 read tag files... INFO @ Tue, 14 Jul 2020 06:59:58: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:00:05: 1000000 INFO @ Tue, 14 Jul 2020 07:00:06: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:00:06: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:00:06: #1 total tags in treatment: 1144702 INFO @ Tue, 14 Jul 2020 07:00:06: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:00:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:00:06: #1 tags after filtering in treatment: 1144702 INFO @ Tue, 14 Jul 2020 07:00:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:00:06: #1 finished! INFO @ Tue, 14 Jul 2020 07:00:06: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:00:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:00:06: #2 number of paired peaks: 573 WARNING @ Tue, 14 Jul 2020 07:00:06: Fewer paired peaks (573) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 573 pairs to build model! INFO @ Tue, 14 Jul 2020 07:00:06: start model_add_line... INFO @ Tue, 14 Jul 2020 07:00:06: start X-correlation... INFO @ Tue, 14 Jul 2020 07:00:06: end of X-cor INFO @ Tue, 14 Jul 2020 07:00:06: #2 finished! INFO @ Tue, 14 Jul 2020 07:00:06: #2 predicted fragment length is 50 bps INFO @ Tue, 14 Jul 2020 07:00:06: #2 alternative fragment length(s) may be 50,200,453,532 bps INFO @ Tue, 14 Jul 2020 07:00:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262229/SRX7262229.20_model.r WARNING @ Tue, 14 Jul 2020 07:00:06: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:00:06: #2 You may need to consider one of the other alternative d(s): 50,200,453,532 WARNING @ Tue, 14 Jul 2020 07:00:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:00:06: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:00:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:00:08: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:00:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262229/SRX7262229.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:00:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262229/SRX7262229.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:00:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262229/SRX7262229.20_summits.bed INFO @ Tue, 14 Jul 2020 07:00:10: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (91 records, 4 fields): 35 millis CompletedMACS2peakCalling