Job ID = 6626389 SRX = SRX7262225 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 2733404 spots for SRR10581848/SRR10581848.sra Written 2733404 spots for SRR10581848/SRR10581848.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626422 ("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: 00:00:34 2733404 reads; of these: 2733404 (100.00%) were unpaired; of these: 635444 (23.25%) aligned 0 times 1753629 (64.16%) aligned exactly 1 time 344331 (12.60%) aligned >1 times 76.75% overall alignment rate Time searching: 00:00:34 Overall time: 00:00:34 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] 66620 / 2097960 = 0.0318 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 06:58:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262225/SRX7262225.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262225/SRX7262225.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262225/SRX7262225.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262225/SRX7262225.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 06:58:51: #1 read tag files... INFO @ Tue, 14 Jul 2020 06:58:51: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 06:58:57: 1000000 INFO @ Tue, 14 Jul 2020 06:59:03: 2000000 INFO @ Tue, 14 Jul 2020 06:59:03: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 06:59:03: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 06:59:03: #1 total tags in treatment: 2031340 INFO @ Tue, 14 Jul 2020 06:59:03: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 06:59:03: #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 06:59:03: #1 tags after filtering in treatment: 2031340 INFO @ Tue, 14 Jul 2020 06:59:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 06:59:03: #1 finished! INFO @ Tue, 14 Jul 2020 06:59:03: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 06:59:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 06:59:03: #2 number of paired peaks: 358 WARNING @ Tue, 14 Jul 2020 06:59:03: Fewer paired peaks (358) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 358 pairs to build model! INFO @ Tue, 14 Jul 2020 06:59:03: start model_add_line... INFO @ Tue, 14 Jul 2020 06:59:03: start X-correlation... INFO @ Tue, 14 Jul 2020 06:59:03: end of X-cor INFO @ Tue, 14 Jul 2020 06:59:03: #2 finished! INFO @ Tue, 14 Jul 2020 06:59:03: #2 predicted fragment length is 50 bps INFO @ Tue, 14 Jul 2020 06:59:03: #2 alternative fragment length(s) may be 50,488 bps INFO @ Tue, 14 Jul 2020 06:59:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262225/SRX7262225.05_model.r WARNING @ Tue, 14 Jul 2020 06:59:03: #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 06:59:03: #2 You may need to consider one of the other alternative d(s): 50,488 WARNING @ Tue, 14 Jul 2020 06:59:03: #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 06:59:03: #3 Call peaks... INFO @ Tue, 14 Jul 2020 06:59:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 06:59:08: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 06:59:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262225/SRX7262225.05_peaks.xls INFO @ Tue, 14 Jul 2020 06:59:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262225/SRX7262225.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 06:59:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262225/SRX7262225.05_summits.bed INFO @ Tue, 14 Jul 2020 06:59:10: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (281 records, 4 fields): 11 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 06:59:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262225/SRX7262225.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262225/SRX7262225.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262225/SRX7262225.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262225/SRX7262225.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 06:59:21: #1 read tag files... INFO @ Tue, 14 Jul 2020 06:59:21: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 06:59:27: 1000000 INFO @ Tue, 14 Jul 2020 06:59:32: 2000000 INFO @ Tue, 14 Jul 2020 06:59:32: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 06:59:32: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 06:59:32: #1 total tags in treatment: 2031340 INFO @ Tue, 14 Jul 2020 06:59:32: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 06:59:32: #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 06:59:32: #1 tags after filtering in treatment: 2031340 INFO @ Tue, 14 Jul 2020 06:59:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 06:59:32: #1 finished! INFO @ Tue, 14 Jul 2020 06:59:32: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 06:59:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 06:59:32: #2 number of paired peaks: 358 WARNING @ Tue, 14 Jul 2020 06:59:32: Fewer paired peaks (358) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 358 pairs to build model! INFO @ Tue, 14 Jul 2020 06:59:32: start model_add_line... INFO @ Tue, 14 Jul 2020 06:59:32: start X-correlation... INFO @ Tue, 14 Jul 2020 06:59:32: end of X-cor INFO @ Tue, 14 Jul 2020 06:59:32: #2 finished! INFO @ Tue, 14 Jul 2020 06:59:32: #2 predicted fragment length is 50 bps INFO @ Tue, 14 Jul 2020 06:59:32: #2 alternative fragment length(s) may be 50,488 bps INFO @ Tue, 14 Jul 2020 06:59:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262225/SRX7262225.10_model.r WARNING @ Tue, 14 Jul 2020 06:59:32: #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 06:59:32: #2 You may need to consider one of the other alternative d(s): 50,488 WARNING @ Tue, 14 Jul 2020 06:59:32: #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 06:59:32: #3 Call peaks... INFO @ Tue, 14 Jul 2020 06:59:32: #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 06:59:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262225/SRX7262225.10_peaks.xls INFO @ Tue, 14 Jul 2020 06:59:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262225/SRX7262225.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 06:59:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262225/SRX7262225.10_summits.bed INFO @ Tue, 14 Jul 2020 06:59:39: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (167 records, 4 fields): 14 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 06:59:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262225/SRX7262225.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262225/SRX7262225.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262225/SRX7262225.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262225/SRX7262225.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 06:59:51: #1 read tag files... INFO @ Tue, 14 Jul 2020 06:59:51: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 06:59:57: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:00:03: 2000000 INFO @ Tue, 14 Jul 2020 07:00:03: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:00:03: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:00:03: #1 total tags in treatment: 2031340 INFO @ Tue, 14 Jul 2020 07:00:03: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:00:03: #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 07:00:03: #1 tags after filtering in treatment: 2031340 INFO @ Tue, 14 Jul 2020 07:00:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:00:03: #1 finished! INFO @ Tue, 14 Jul 2020 07:00:03: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:00:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:00:03: #2 number of paired peaks: 358 WARNING @ Tue, 14 Jul 2020 07:00:03: Fewer paired peaks (358) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 358 pairs to build model! INFO @ Tue, 14 Jul 2020 07:00:03: start model_add_line... INFO @ Tue, 14 Jul 2020 07:00:03: start X-correlation... INFO @ Tue, 14 Jul 2020 07:00:03: end of X-cor INFO @ Tue, 14 Jul 2020 07:00:03: #2 finished! INFO @ Tue, 14 Jul 2020 07:00:03: #2 predicted fragment length is 50 bps INFO @ Tue, 14 Jul 2020 07:00:03: #2 alternative fragment length(s) may be 50,488 bps INFO @ Tue, 14 Jul 2020 07:00:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262225/SRX7262225.20_model.r WARNING @ Tue, 14 Jul 2020 07:00:04: #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 07:00:04: #2 You may need to consider one of the other alternative d(s): 50,488 WARNING @ Tue, 14 Jul 2020 07:00:04: #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 07:00:04: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:00:04: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:00:08: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:00:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262225/SRX7262225.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:00:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262225/SRX7262225.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:00:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262225/SRX7262225.20_summits.bed INFO @ Tue, 14 Jul 2020 07:00:10: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (59 records, 4 fields): 14 millis CompletedMACS2peakCalling