Job ID = 6626381 SRX = SRX7262218 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 8695122 spots for SRR10581841/SRR10581841.sra Written 8695122 spots for SRR10581841/SRR10581841.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626460 ("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: 00:01:43 8695122 reads; of these: 8695122 (100.00%) were unpaired; of these: 1039425 (11.95%) aligned 0 times 6016054 (69.19%) aligned exactly 1 time 1639643 (18.86%) aligned >1 times 88.05% overall alignment rate Time searching: 00:01:43 Overall time: 00:01:43 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] 1431247 / 7655697 = 0.1870 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 07:01:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262218/SRX7262218.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262218/SRX7262218.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262218/SRX7262218.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262218/SRX7262218.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 07:01:12: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:01:12: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:01:18: 1000000 INFO @ Tue, 14 Jul 2020 07:01:24: 2000000 INFO @ Tue, 14 Jul 2020 07:01:29: 3000000 INFO @ Tue, 14 Jul 2020 07:01:35: 4000000 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 07:01:41: 5000000 INFO @ Tue, 14 Jul 2020 07:01:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262218/SRX7262218.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262218/SRX7262218.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262218/SRX7262218.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262218/SRX7262218.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 07:01:42: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:01:42: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:01:47: 6000000 INFO @ Tue, 14 Jul 2020 07:01:48: 1000000 INFO @ Tue, 14 Jul 2020 07:01:48: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:01:48: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:01:48: #1 total tags in treatment: 6224450 INFO @ Tue, 14 Jul 2020 07:01:48: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:01:48: #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 07:01:49: #1 tags after filtering in treatment: 6224450 INFO @ Tue, 14 Jul 2020 07:01:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:01:49: #1 finished! INFO @ Tue, 14 Jul 2020 07:01:49: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:01:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:01:49: #2 number of paired peaks: 474 WARNING @ Tue, 14 Jul 2020 07:01:49: Fewer paired peaks (474) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 474 pairs to build model! INFO @ Tue, 14 Jul 2020 07:01:49: start model_add_line... INFO @ Tue, 14 Jul 2020 07:01:49: start X-correlation... INFO @ Tue, 14 Jul 2020 07:01:49: end of X-cor INFO @ Tue, 14 Jul 2020 07:01:49: #2 finished! INFO @ Tue, 14 Jul 2020 07:01:49: #2 predicted fragment length is 50 bps INFO @ Tue, 14 Jul 2020 07:01:49: #2 alternative fragment length(s) may be 4,50,537 bps INFO @ Tue, 14 Jul 2020 07:01:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262218/SRX7262218.05_model.r WARNING @ Tue, 14 Jul 2020 07:01:49: #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 07:01:49: #2 You may need to consider one of the other alternative d(s): 4,50,537 WARNING @ Tue, 14 Jul 2020 07:01:49: #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 07:01:49: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:01:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:01:54: 2000000 INFO @ Tue, 14 Jul 2020 07:02:00: 3000000 INFO @ Tue, 14 Jul 2020 07:02:02: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:02:06: 4000000 INFO @ Tue, 14 Jul 2020 07:02:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262218/SRX7262218.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:02:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262218/SRX7262218.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:02:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262218/SRX7262218.05_summits.bed INFO @ Tue, 14 Jul 2020 07:02:08: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (590 records, 4 fields): 13 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 07:02:12: 5000000 INFO @ Tue, 14 Jul 2020 07:02:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262218/SRX7262218.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262218/SRX7262218.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262218/SRX7262218.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262218/SRX7262218.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 07:02:12: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:02:12: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:02:18: 6000000 INFO @ Tue, 14 Jul 2020 07:02:18: 1000000 INFO @ Tue, 14 Jul 2020 07:02:19: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:02:19: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:02:19: #1 total tags in treatment: 6224450 INFO @ Tue, 14 Jul 2020 07:02:19: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:02:19: #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 07:02:19: #1 tags after filtering in treatment: 6224450 INFO @ Tue, 14 Jul 2020 07:02:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:02:19: #1 finished! INFO @ Tue, 14 Jul 2020 07:02:19: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:02:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:02:20: #2 number of paired peaks: 474 WARNING @ Tue, 14 Jul 2020 07:02:20: Fewer paired peaks (474) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 474 pairs to build model! INFO @ Tue, 14 Jul 2020 07:02:20: start model_add_line... INFO @ Tue, 14 Jul 2020 07:02:20: start X-correlation... INFO @ Tue, 14 Jul 2020 07:02:20: end of X-cor INFO @ Tue, 14 Jul 2020 07:02:20: #2 finished! INFO @ Tue, 14 Jul 2020 07:02:20: #2 predicted fragment length is 50 bps INFO @ Tue, 14 Jul 2020 07:02:20: #2 alternative fragment length(s) may be 4,50,537 bps INFO @ Tue, 14 Jul 2020 07:02:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262218/SRX7262218.10_model.r WARNING @ Tue, 14 Jul 2020 07:02:20: #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 07:02:20: #2 You may need to consider one of the other alternative d(s): 4,50,537 WARNING @ Tue, 14 Jul 2020 07:02:20: #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 07:02:20: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:02:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:02:24: 2000000 INFO @ Tue, 14 Jul 2020 07:02:30: 3000000 INFO @ Tue, 14 Jul 2020 07:02:32: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:02:36: 4000000 INFO @ Tue, 14 Jul 2020 07:02:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262218/SRX7262218.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:02:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262218/SRX7262218.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:02:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262218/SRX7262218.10_summits.bed INFO @ Tue, 14 Jul 2020 07:02:39: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (389 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:02:42: 5000000 INFO @ Tue, 14 Jul 2020 07:02:48: 6000000 INFO @ Tue, 14 Jul 2020 07:02:49: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:02:49: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:02:49: #1 total tags in treatment: 6224450 INFO @ Tue, 14 Jul 2020 07:02:49: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:02:49: #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 07:02:49: #1 tags after filtering in treatment: 6224450 INFO @ Tue, 14 Jul 2020 07:02:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:02:49: #1 finished! INFO @ Tue, 14 Jul 2020 07:02:49: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:02:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:02:50: #2 number of paired peaks: 474 WARNING @ Tue, 14 Jul 2020 07:02:50: Fewer paired peaks (474) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 474 pairs to build model! INFO @ Tue, 14 Jul 2020 07:02:50: start model_add_line... INFO @ Tue, 14 Jul 2020 07:02:50: start X-correlation... INFO @ Tue, 14 Jul 2020 07:02:50: end of X-cor INFO @ Tue, 14 Jul 2020 07:02:50: #2 finished! INFO @ Tue, 14 Jul 2020 07:02:50: #2 predicted fragment length is 50 bps INFO @ Tue, 14 Jul 2020 07:02:50: #2 alternative fragment length(s) may be 4,50,537 bps INFO @ Tue, 14 Jul 2020 07:02:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262218/SRX7262218.20_model.r WARNING @ Tue, 14 Jul 2020 07:02:50: #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 07:02:50: #2 You may need to consider one of the other alternative d(s): 4,50,537 WARNING @ Tue, 14 Jul 2020 07:02:50: #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 07:02:50: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:02:50: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:03:03: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:03:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262218/SRX7262218.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:03:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262218/SRX7262218.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:03:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262218/SRX7262218.20_summits.bed INFO @ Tue, 14 Jul 2020 07:03:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (159 records, 4 fields): 10 millis CompletedMACS2peakCalling