Job ID = 6626379 SRX = SRX7262216 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 5872918 spots for SRR10581839/SRR10581839.sra Written 5872918 spots for SRR10581839/SRR10581839.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626444 ("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: 00:01:24 5872918 reads; of these: 5872918 (100.00%) were unpaired; of these: 354087 (6.03%) aligned 0 times 4331176 (73.75%) aligned exactly 1 time 1187655 (20.22%) aligned >1 times 93.97% overall alignment rate Time searching: 00:01:24 Overall time: 00:01:24 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] 469185 / 5518831 = 0.0850 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 06:59:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262216/SRX7262216.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262216/SRX7262216.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262216/SRX7262216.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262216/SRX7262216.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 06:59:55: #1 read tag files... INFO @ Tue, 14 Jul 2020 06:59:55: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:00:00: 1000000 INFO @ Tue, 14 Jul 2020 07:00:04: 2000000 INFO @ Tue, 14 Jul 2020 07:00:09: 3000000 INFO @ Tue, 14 Jul 2020 07:00:14: 4000000 INFO @ Tue, 14 Jul 2020 07:00:19: 5000000 INFO @ Tue, 14 Jul 2020 07:00:19: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:00:19: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:00:19: #1 total tags in treatment: 5049646 INFO @ Tue, 14 Jul 2020 07:00:19: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:00:19: #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 07:00:19: #1 tags after filtering in treatment: 5049646 INFO @ Tue, 14 Jul 2020 07:00:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:00:19: #1 finished! INFO @ Tue, 14 Jul 2020 07:00:19: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:00:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:00:20: #2 number of paired peaks: 432 WARNING @ Tue, 14 Jul 2020 07:00:20: Fewer paired peaks (432) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 432 pairs to build model! INFO @ Tue, 14 Jul 2020 07:00:20: start model_add_line... INFO @ Tue, 14 Jul 2020 07:00:20: start X-correlation... INFO @ Tue, 14 Jul 2020 07:00:20: end of X-cor INFO @ Tue, 14 Jul 2020 07:00:20: #2 finished! INFO @ Tue, 14 Jul 2020 07:00:20: #2 predicted fragment length is 49 bps INFO @ Tue, 14 Jul 2020 07:00:20: #2 alternative fragment length(s) may be 49 bps INFO @ Tue, 14 Jul 2020 07:00:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262216/SRX7262216.05_model.r WARNING @ Tue, 14 Jul 2020 07:00:20: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:00:20: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Tue, 14 Jul 2020 07:00:20: #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 07:00:20: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:00:20: #3 Pre-compute pvalue-qvalue table... 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 07:00:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262216/SRX7262216.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262216/SRX7262216.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262216/SRX7262216.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262216/SRX7262216.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 07:00:24: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:00:24: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:00:29: 1000000 INFO @ Tue, 14 Jul 2020 07:00:30: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:00:34: 2000000 INFO @ Tue, 14 Jul 2020 07:00:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262216/SRX7262216.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:00:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262216/SRX7262216.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:00:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262216/SRX7262216.05_summits.bed INFO @ Tue, 14 Jul 2020 07:00:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (599 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:00:39: 3000000 INFO @ Tue, 14 Jul 2020 07:00:44: 4000000 INFO @ Tue, 14 Jul 2020 07:00:49: 5000000 INFO @ Tue, 14 Jul 2020 07:00:49: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:00:49: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:00:49: #1 total tags in treatment: 5049646 INFO @ Tue, 14 Jul 2020 07:00:49: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:00:49: #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 07:00:49: #1 tags after filtering in treatment: 5049646 INFO @ Tue, 14 Jul 2020 07:00:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:00:49: #1 finished! INFO @ Tue, 14 Jul 2020 07:00:49: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:00:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:00:50: #2 number of paired peaks: 432 WARNING @ Tue, 14 Jul 2020 07:00:50: Fewer paired peaks (432) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 432 pairs to build model! INFO @ Tue, 14 Jul 2020 07:00:50: start model_add_line... INFO @ Tue, 14 Jul 2020 07:00:50: start X-correlation... INFO @ Tue, 14 Jul 2020 07:00:50: end of X-cor INFO @ Tue, 14 Jul 2020 07:00:50: #2 finished! INFO @ Tue, 14 Jul 2020 07:00:50: #2 predicted fragment length is 49 bps INFO @ Tue, 14 Jul 2020 07:00:50: #2 alternative fragment length(s) may be 49 bps INFO @ Tue, 14 Jul 2020 07:00:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262216/SRX7262216.10_model.r WARNING @ Tue, 14 Jul 2020 07:00:50: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:00:50: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Tue, 14 Jul 2020 07:00:50: #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 07:00:50: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:00:50: #3 Pre-compute pvalue-qvalue table... 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 07:00:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262216/SRX7262216.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262216/SRX7262216.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262216/SRX7262216.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262216/SRX7262216.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 07:00:54: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:00:54: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:01:00: 1000000 INFO @ Tue, 14 Jul 2020 07:01:00: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:01:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262216/SRX7262216.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:01:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262216/SRX7262216.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:01:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262216/SRX7262216.10_summits.bed INFO @ Tue, 14 Jul 2020 07:01:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (378 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:01:06: 2000000 INFO @ Tue, 14 Jul 2020 07:01:11: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:01:17: 4000000 INFO @ Tue, 14 Jul 2020 07:01:23: 5000000 INFO @ Tue, 14 Jul 2020 07:01:23: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:01:23: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:01:23: #1 total tags in treatment: 5049646 INFO @ Tue, 14 Jul 2020 07:01:23: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:01:23: #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 07:01:23: #1 tags after filtering in treatment: 5049646 INFO @ Tue, 14 Jul 2020 07:01:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:01:23: #1 finished! INFO @ Tue, 14 Jul 2020 07:01:23: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:01:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:01:24: #2 number of paired peaks: 432 WARNING @ Tue, 14 Jul 2020 07:01:24: Fewer paired peaks (432) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 432 pairs to build model! INFO @ Tue, 14 Jul 2020 07:01:24: start model_add_line... INFO @ Tue, 14 Jul 2020 07:01:24: start X-correlation... INFO @ Tue, 14 Jul 2020 07:01:24: end of X-cor INFO @ Tue, 14 Jul 2020 07:01:24: #2 finished! INFO @ Tue, 14 Jul 2020 07:01:24: #2 predicted fragment length is 49 bps INFO @ Tue, 14 Jul 2020 07:01:24: #2 alternative fragment length(s) may be 49 bps INFO @ Tue, 14 Jul 2020 07:01:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262216/SRX7262216.20_model.r WARNING @ Tue, 14 Jul 2020 07:01:24: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:01:24: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Tue, 14 Jul 2020 07:01:24: #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 07:01:24: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:01:24: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:01:34: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:01:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262216/SRX7262216.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:01:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262216/SRX7262216.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:01:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262216/SRX7262216.20_summits.bed INFO @ Tue, 14 Jul 2020 07:01:40: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (169 records, 4 fields): 14 millis CompletedMACS2peakCalling