Job ID = 6626387 SRX = SRX7262223 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 4361308 spots for SRR10581846/SRR10581846.sra Written 4361308 spots for SRR10581846/SRR10581846.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626424 ("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: 00:00:48 4361308 reads; of these: 4361308 (100.00%) were unpaired; of these: 1161596 (26.63%) aligned 0 times 2566408 (58.84%) aligned exactly 1 time 633304 (14.52%) aligned >1 times 73.37% overall alignment rate Time searching: 00:00:48 Overall time: 00:00:48 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] 1027455 / 3199712 = 0.3211 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 06:59:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262223/SRX7262223.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262223/SRX7262223.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262223/SRX7262223.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262223/SRX7262223.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 06:59:14: #1 read tag files... INFO @ Tue, 14 Jul 2020 06:59:14: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 06:59:19: 1000000 INFO @ Tue, 14 Jul 2020 06:59:24: 2000000 INFO @ Tue, 14 Jul 2020 06:59:25: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 06:59:25: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 06:59:25: #1 total tags in treatment: 2172257 INFO @ Tue, 14 Jul 2020 06:59:25: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 06:59:25: #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 06:59:25: #1 tags after filtering in treatment: 2172257 INFO @ Tue, 14 Jul 2020 06:59:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 06:59:25: #1 finished! INFO @ Tue, 14 Jul 2020 06:59:25: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 06:59:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 06:59:25: #2 number of paired peaks: 568 WARNING @ Tue, 14 Jul 2020 06:59:25: Fewer paired peaks (568) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 568 pairs to build model! INFO @ Tue, 14 Jul 2020 06:59:25: start model_add_line... INFO @ Tue, 14 Jul 2020 06:59:25: start X-correlation... INFO @ Tue, 14 Jul 2020 06:59:25: end of X-cor INFO @ Tue, 14 Jul 2020 06:59:25: #2 finished! INFO @ Tue, 14 Jul 2020 06:59:25: #2 predicted fragment length is 48 bps INFO @ Tue, 14 Jul 2020 06:59:25: #2 alternative fragment length(s) may be 48,187,460 bps INFO @ Tue, 14 Jul 2020 06:59:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262223/SRX7262223.05_model.r WARNING @ Tue, 14 Jul 2020 06:59:25: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 06:59:25: #2 You may need to consider one of the other alternative d(s): 48,187,460 WARNING @ Tue, 14 Jul 2020 06:59:25: #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 06:59:25: #3 Call peaks... INFO @ Tue, 14 Jul 2020 06:59:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 06:59:30: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 06:59:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262223/SRX7262223.05_peaks.xls INFO @ Tue, 14 Jul 2020 06:59:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262223/SRX7262223.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 06:59:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262223/SRX7262223.05_summits.bed INFO @ Tue, 14 Jul 2020 06:59:33: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (471 records, 4 fields): 21 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 06:59:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262223/SRX7262223.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262223/SRX7262223.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262223/SRX7262223.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262223/SRX7262223.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 06:59:44: #1 read tag files... INFO @ Tue, 14 Jul 2020 06:59:44: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 06:59:49: 1000000 INFO @ Tue, 14 Jul 2020 06:59:55: 2000000 INFO @ Tue, 14 Jul 2020 06:59:56: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 06:59:56: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 06:59:56: #1 total tags in treatment: 2172257 INFO @ Tue, 14 Jul 2020 06:59:56: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 06:59:56: #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 06:59:56: #1 tags after filtering in treatment: 2172257 INFO @ Tue, 14 Jul 2020 06:59:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 06:59:56: #1 finished! INFO @ Tue, 14 Jul 2020 06:59:56: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 06:59:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 06:59:56: #2 number of paired peaks: 568 WARNING @ Tue, 14 Jul 2020 06:59:56: Fewer paired peaks (568) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 568 pairs to build model! INFO @ Tue, 14 Jul 2020 06:59:56: start model_add_line... INFO @ Tue, 14 Jul 2020 06:59:56: start X-correlation... INFO @ Tue, 14 Jul 2020 06:59:56: end of X-cor INFO @ Tue, 14 Jul 2020 06:59:56: #2 finished! INFO @ Tue, 14 Jul 2020 06:59:56: #2 predicted fragment length is 48 bps INFO @ Tue, 14 Jul 2020 06:59:56: #2 alternative fragment length(s) may be 48,187,460 bps INFO @ Tue, 14 Jul 2020 06:59:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262223/SRX7262223.10_model.r WARNING @ Tue, 14 Jul 2020 06:59:56: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 06:59:56: #2 You may need to consider one of the other alternative d(s): 48,187,460 WARNING @ Tue, 14 Jul 2020 06:59:56: #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 06:59:56: #3 Call peaks... INFO @ Tue, 14 Jul 2020 06:59:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:00:01: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:00:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262223/SRX7262223.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:00:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262223/SRX7262223.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:00:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262223/SRX7262223.10_summits.bed INFO @ Tue, 14 Jul 2020 07:00:03: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (279 records, 4 fields): 17 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 07:00:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262223/SRX7262223.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262223/SRX7262223.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262223/SRX7262223.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262223/SRX7262223.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 07:00:14: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:00:14: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:00:19: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:00:24: 2000000 INFO @ Tue, 14 Jul 2020 07:00:25: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:00:25: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:00:25: #1 total tags in treatment: 2172257 INFO @ Tue, 14 Jul 2020 07:00:25: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:00:25: #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 07:00:25: #1 tags after filtering in treatment: 2172257 INFO @ Tue, 14 Jul 2020 07:00:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:00:25: #1 finished! INFO @ Tue, 14 Jul 2020 07:00:25: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:00:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:00:25: #2 number of paired peaks: 568 WARNING @ Tue, 14 Jul 2020 07:00:25: Fewer paired peaks (568) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 568 pairs to build model! INFO @ Tue, 14 Jul 2020 07:00:25: start model_add_line... INFO @ Tue, 14 Jul 2020 07:00:25: start X-correlation... INFO @ Tue, 14 Jul 2020 07:00:25: end of X-cor INFO @ Tue, 14 Jul 2020 07:00:25: #2 finished! INFO @ Tue, 14 Jul 2020 07:00:25: #2 predicted fragment length is 48 bps INFO @ Tue, 14 Jul 2020 07:00:25: #2 alternative fragment length(s) may be 48,187,460 bps INFO @ Tue, 14 Jul 2020 07:00:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262223/SRX7262223.20_model.r WARNING @ Tue, 14 Jul 2020 07:00:25: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:00:25: #2 You may need to consider one of the other alternative d(s): 48,187,460 WARNING @ Tue, 14 Jul 2020 07:00:25: #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 07:00:25: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:00:25: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:00:30: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:00:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262223/SRX7262223.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:00:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262223/SRX7262223.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:00:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262223/SRX7262223.20_summits.bed INFO @ Tue, 14 Jul 2020 07:00:32: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (113 records, 4 fields): 18 millis CompletedMACS2peakCalling