Job ID = 14160724 SRX = SRX10569209 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2021-12-08T18:53:16 prefetch.2.10.7: 1) Downloading 'SRR14202283'... 2021-12-08T18:53:16 prefetch.2.10.7: Downloading via HTTPS... 2021-12-08T18:55:47 prefetch.2.10.7: HTTPS download succeed 2021-12-08T18:55:47 prefetch.2.10.7: 1) 'SRR14202283' was downloaded successfully 2021-12-08T18:55:47 prefetch.2.10.7: 'SRR14202283' has 0 unresolved dependencies Read 24113423 spots for SRR14202283/SRR14202283.sra Written 24113423 spots for SRR14202283/SRR14202283.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160846 ("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: 00:03:38 24113423 reads; of these: 24113423 (100.00%) were unpaired; of these: 22885809 (94.91%) aligned 0 times 967836 (4.01%) aligned exactly 1 time 259778 (1.08%) aligned >1 times 5.09% overall alignment rate Time searching: 00:03:38 Overall time: 00:03:38 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] 69147 / 1227614 = 0.0563 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 04:02:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10569209/SRX10569209.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10569209/SRX10569209.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10569209/SRX10569209.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10569209/SRX10569209.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 @ Thu, 09 Dec 2021 04:02:50: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:02:50: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:03:02: 1000000 INFO @ Thu, 09 Dec 2021 04:03:03: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 04:03:03: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 04:03:03: #1 total tags in treatment: 1158467 INFO @ Thu, 09 Dec 2021 04:03:03: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:03:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 04:03:03: #1 tags after filtering in treatment: 1158467 INFO @ Thu, 09 Dec 2021 04:03:03: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:03:03: #1 finished! INFO @ Thu, 09 Dec 2021 04:03:03: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:03:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:03:03: #2 number of paired peaks: 513 WARNING @ Thu, 09 Dec 2021 04:03:03: Fewer paired peaks (513) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 513 pairs to build model! INFO @ Thu, 09 Dec 2021 04:03:03: start model_add_line... INFO @ Thu, 09 Dec 2021 04:03:03: start X-correlation... INFO @ Thu, 09 Dec 2021 04:03:03: end of X-cor INFO @ Thu, 09 Dec 2021 04:03:03: #2 finished! INFO @ Thu, 09 Dec 2021 04:03:03: #2 predicted fragment length is 68 bps INFO @ Thu, 09 Dec 2021 04:03:03: #2 alternative fragment length(s) may be 68,546,566 bps INFO @ Thu, 09 Dec 2021 04:03:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10569209/SRX10569209.05_model.r WARNING @ Thu, 09 Dec 2021 04:03:03: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:03:03: #2 You may need to consider one of the other alternative d(s): 68,546,566 WARNING @ Thu, 09 Dec 2021 04:03:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 04:03:03: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:03:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:03:07: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:03:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10569209/SRX10569209.05_peaks.xls INFO @ Thu, 09 Dec 2021 04:03:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10569209/SRX10569209.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:03:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10569209/SRX10569209.05_summits.bed INFO @ Thu, 09 Dec 2021 04:03:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (320 records, 4 fields): 2 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 04:03:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10569209/SRX10569209.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10569209/SRX10569209.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10569209/SRX10569209.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10569209/SRX10569209.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 @ Thu, 09 Dec 2021 04:03:20: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:03:20: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:03:32: 1000000 INFO @ Thu, 09 Dec 2021 04:03:34: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 04:03:34: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 04:03:34: #1 total tags in treatment: 1158467 INFO @ Thu, 09 Dec 2021 04:03:34: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:03:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 04:03:34: #1 tags after filtering in treatment: 1158467 INFO @ Thu, 09 Dec 2021 04:03:34: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:03:34: #1 finished! INFO @ Thu, 09 Dec 2021 04:03:34: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:03:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:03:34: #2 number of paired peaks: 513 WARNING @ Thu, 09 Dec 2021 04:03:34: Fewer paired peaks (513) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 513 pairs to build model! INFO @ Thu, 09 Dec 2021 04:03:34: start model_add_line... INFO @ Thu, 09 Dec 2021 04:03:34: start X-correlation... INFO @ Thu, 09 Dec 2021 04:03:34: end of X-cor INFO @ Thu, 09 Dec 2021 04:03:34: #2 finished! INFO @ Thu, 09 Dec 2021 04:03:34: #2 predicted fragment length is 68 bps INFO @ Thu, 09 Dec 2021 04:03:34: #2 alternative fragment length(s) may be 68,546,566 bps INFO @ Thu, 09 Dec 2021 04:03:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10569209/SRX10569209.10_model.r WARNING @ Thu, 09 Dec 2021 04:03:34: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:03:34: #2 You may need to consider one of the other alternative d(s): 68,546,566 WARNING @ Thu, 09 Dec 2021 04:03:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 04:03:34: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:03:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:03:38: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:03:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10569209/SRX10569209.10_peaks.xls INFO @ Thu, 09 Dec 2021 04:03:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10569209/SRX10569209.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:03:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10569209/SRX10569209.10_summits.bed INFO @ Thu, 09 Dec 2021 04:03:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (203 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 04:03:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10569209/SRX10569209.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10569209/SRX10569209.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10569209/SRX10569209.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10569209/SRX10569209.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 @ Thu, 09 Dec 2021 04:03:50: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:03:50: #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 @ Thu, 09 Dec 2021 04:04:02: 1000000 INFO @ Thu, 09 Dec 2021 04:04:03: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 04:04:03: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 04:04:03: #1 total tags in treatment: 1158467 INFO @ Thu, 09 Dec 2021 04:04:03: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:04:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 04:04:03: #1 tags after filtering in treatment: 1158467 INFO @ Thu, 09 Dec 2021 04:04:03: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:04:03: #1 finished! INFO @ Thu, 09 Dec 2021 04:04:03: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:04:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:04:03: #2 number of paired peaks: 513 WARNING @ Thu, 09 Dec 2021 04:04:03: Fewer paired peaks (513) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 513 pairs to build model! INFO @ Thu, 09 Dec 2021 04:04:03: start model_add_line... INFO @ Thu, 09 Dec 2021 04:04:03: start X-correlation... INFO @ Thu, 09 Dec 2021 04:04:03: end of X-cor INFO @ Thu, 09 Dec 2021 04:04:03: #2 finished! INFO @ Thu, 09 Dec 2021 04:04:03: #2 predicted fragment length is 68 bps INFO @ Thu, 09 Dec 2021 04:04:03: #2 alternative fragment length(s) may be 68,546,566 bps INFO @ Thu, 09 Dec 2021 04:04:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10569209/SRX10569209.20_model.r WARNING @ Thu, 09 Dec 2021 04:04:03: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:04:03: #2 You may need to consider one of the other alternative d(s): 68,546,566 WARNING @ Thu, 09 Dec 2021 04:04:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 04:04:03: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:04:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:04:07: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:04:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10569209/SRX10569209.20_peaks.xls INFO @ Thu, 09 Dec 2021 04:04:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10569209/SRX10569209.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:04:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10569209/SRX10569209.20_summits.bed INFO @ Thu, 09 Dec 2021 04:04:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (93 records, 4 fields): 2 millis CompletedMACS2peakCalling