Job ID = 6626357 SRX = SRX7262197 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 9157221 spots for SRR10581820/SRR10581820.sra Written 9157221 spots for SRR10581820/SRR10581820.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626439 ("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: 00:02:06 9157221 reads; of these: 9157221 (100.00%) were unpaired; of these: 350627 (3.83%) aligned 0 times 7147074 (78.05%) aligned exactly 1 time 1659520 (18.12%) aligned >1 times 96.17% overall alignment rate Time searching: 00:02:06 Overall time: 00:02:06 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] 771972 / 8806594 = 0.0877 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 07:00:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262197/SRX7262197.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262197/SRX7262197.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262197/SRX7262197.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262197/SRX7262197.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 07:00:26: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:00:26: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:00:31: 1000000 INFO @ Tue, 14 Jul 2020 07:00:36: 2000000 INFO @ Tue, 14 Jul 2020 07:00:41: 3000000 INFO @ Tue, 14 Jul 2020 07:00:46: 4000000 INFO @ Tue, 14 Jul 2020 07:00:51: 5000000 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 07:00:56: 6000000 INFO @ Tue, 14 Jul 2020 07:00:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262197/SRX7262197.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262197/SRX7262197.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262197/SRX7262197.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262197/SRX7262197.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 07:00:56: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:00:56: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:01:01: 7000000 INFO @ Tue, 14 Jul 2020 07:01:01: 1000000 INFO @ Tue, 14 Jul 2020 07:01:06: 8000000 INFO @ Tue, 14 Jul 2020 07:01:06: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:01:06: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:01:06: #1 total tags in treatment: 8034622 INFO @ Tue, 14 Jul 2020 07:01:06: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:01:06: #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 07:01:06: #1 tags after filtering in treatment: 8034622 INFO @ Tue, 14 Jul 2020 07:01:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:01:06: #1 finished! INFO @ Tue, 14 Jul 2020 07:01:06: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:01:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:01:06: 2000000 INFO @ Tue, 14 Jul 2020 07:01:07: #2 number of paired peaks: 304 WARNING @ Tue, 14 Jul 2020 07:01:07: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Tue, 14 Jul 2020 07:01:07: start model_add_line... INFO @ Tue, 14 Jul 2020 07:01:07: start X-correlation... INFO @ Tue, 14 Jul 2020 07:01:07: end of X-cor INFO @ Tue, 14 Jul 2020 07:01:07: #2 finished! INFO @ Tue, 14 Jul 2020 07:01:07: #2 predicted fragment length is 46 bps INFO @ Tue, 14 Jul 2020 07:01:07: #2 alternative fragment length(s) may be 3,46 bps INFO @ Tue, 14 Jul 2020 07:01:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262197/SRX7262197.05_model.r WARNING @ Tue, 14 Jul 2020 07:01:07: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:01:07: #2 You may need to consider one of the other alternative d(s): 3,46 WARNING @ Tue, 14 Jul 2020 07:01:07: #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 07:01:07: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:01:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:01:11: 3000000 INFO @ Tue, 14 Jul 2020 07:01:16: 4000000 INFO @ Tue, 14 Jul 2020 07:01:21: 5000000 INFO @ Tue, 14 Jul 2020 07:01:23: #3 Call peaks for each chromosome... 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 07:01:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262197/SRX7262197.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262197/SRX7262197.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262197/SRX7262197.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262197/SRX7262197.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 07:01:26: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:01:26: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:01:26: 6000000 INFO @ Tue, 14 Jul 2020 07:01:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262197/SRX7262197.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:01:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262197/SRX7262197.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:01:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262197/SRX7262197.05_summits.bed INFO @ Tue, 14 Jul 2020 07:01:30: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (632 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:01:31: 1000000 INFO @ Tue, 14 Jul 2020 07:01:31: 7000000 INFO @ Tue, 14 Jul 2020 07:01:36: 2000000 INFO @ Tue, 14 Jul 2020 07:01:36: 8000000 INFO @ Tue, 14 Jul 2020 07:01:37: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:01:37: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:01:37: #1 total tags in treatment: 8034622 INFO @ Tue, 14 Jul 2020 07:01:37: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:01:37: #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 07:01:37: #1 tags after filtering in treatment: 8034622 INFO @ Tue, 14 Jul 2020 07:01:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:01:37: #1 finished! INFO @ Tue, 14 Jul 2020 07:01:37: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:01:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:01:37: #2 number of paired peaks: 304 WARNING @ Tue, 14 Jul 2020 07:01:37: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Tue, 14 Jul 2020 07:01:37: start model_add_line... INFO @ Tue, 14 Jul 2020 07:01:37: start X-correlation... INFO @ Tue, 14 Jul 2020 07:01:37: end of X-cor INFO @ Tue, 14 Jul 2020 07:01:37: #2 finished! INFO @ Tue, 14 Jul 2020 07:01:37: #2 predicted fragment length is 46 bps INFO @ Tue, 14 Jul 2020 07:01:37: #2 alternative fragment length(s) may be 3,46 bps INFO @ Tue, 14 Jul 2020 07:01:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262197/SRX7262197.10_model.r WARNING @ Tue, 14 Jul 2020 07:01:37: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:01:37: #2 You may need to consider one of the other alternative d(s): 3,46 WARNING @ Tue, 14 Jul 2020 07:01:37: #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 07:01:37: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:01:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:01:41: 3000000 INFO @ Tue, 14 Jul 2020 07:01:46: 4000000 INFO @ Tue, 14 Jul 2020 07:01:51: 5000000 INFO @ Tue, 14 Jul 2020 07:01:54: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:01:56: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:02:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262197/SRX7262197.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:02:01: 7000000 INFO @ Tue, 14 Jul 2020 07:02:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262197/SRX7262197.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:02:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262197/SRX7262197.10_summits.bed INFO @ Tue, 14 Jul 2020 07:02:01: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (405 records, 4 fields): 51 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:02:06: 8000000 INFO @ Tue, 14 Jul 2020 07:02:06: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:02:06: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:02:06: #1 total tags in treatment: 8034622 INFO @ Tue, 14 Jul 2020 07:02:06: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:02:06: #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 07:02:06: #1 tags after filtering in treatment: 8034622 INFO @ Tue, 14 Jul 2020 07:02:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:02:06: #1 finished! INFO @ Tue, 14 Jul 2020 07:02:06: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:02:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:02:07: #2 number of paired peaks: 304 WARNING @ Tue, 14 Jul 2020 07:02:07: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Tue, 14 Jul 2020 07:02:07: start model_add_line... INFO @ Tue, 14 Jul 2020 07:02:07: start X-correlation... INFO @ Tue, 14 Jul 2020 07:02:07: end of X-cor INFO @ Tue, 14 Jul 2020 07:02:07: #2 finished! INFO @ Tue, 14 Jul 2020 07:02:07: #2 predicted fragment length is 46 bps INFO @ Tue, 14 Jul 2020 07:02:07: #2 alternative fragment length(s) may be 3,46 bps INFO @ Tue, 14 Jul 2020 07:02:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262197/SRX7262197.20_model.r WARNING @ Tue, 14 Jul 2020 07:02:07: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:02:07: #2 You may need to consider one of the other alternative d(s): 3,46 WARNING @ Tue, 14 Jul 2020 07:02:07: #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 07:02:07: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:02:07: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:02:23: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:02:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262197/SRX7262197.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:02:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262197/SRX7262197.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:02:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262197/SRX7262197.20_summits.bed INFO @ Tue, 14 Jul 2020 07:02:31: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (164 records, 4 fields): 55 millis CompletedMACS2peakCalling