Job ID = 6366490 SRX = SRX147642 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:47:22 prefetch.2.10.7: 1) Downloading 'SRR496319'... 2020-06-15T22:47:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:47:51 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:47:51 prefetch.2.10.7: 'SRR496319' is valid 2020-06-15T22:47:51 prefetch.2.10.7: 1) 'SRR496319' was downloaded successfully Read 6026182 spots for SRR496319/SRR496319.sra Written 6026182 spots for SRR496319/SRR496319.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:51 6026182 reads; of these: 6026182 (100.00%) were unpaired; of these: 1862389 (30.90%) aligned 0 times 3459822 (57.41%) aligned exactly 1 time 703971 (11.68%) aligned >1 times 69.10% overall alignment rate Time searching: 00:00:51 Overall time: 00:00:51 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] 532866 / 4163793 = 0.1280 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, 16 Jun 2020 07:50:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX147642/SRX147642.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX147642/SRX147642.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX147642/SRX147642.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX147642/SRX147642.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, 16 Jun 2020 07:50:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:50:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:50:26: 1000000 INFO @ Tue, 16 Jun 2020 07:50:31: 2000000 INFO @ Tue, 16 Jun 2020 07:50:36: 3000000 INFO @ Tue, 16 Jun 2020 07:50:39: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:50:39: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:50:39: #1 total tags in treatment: 3630927 INFO @ Tue, 16 Jun 2020 07:50:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:50:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:50:39: #1 tags after filtering in treatment: 3630927 INFO @ Tue, 16 Jun 2020 07:50:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:50:39: #1 finished! INFO @ Tue, 16 Jun 2020 07:50:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:50:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:50:39: #2 number of paired peaks: 469 WARNING @ Tue, 16 Jun 2020 07:50:39: Fewer paired peaks (469) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 469 pairs to build model! INFO @ Tue, 16 Jun 2020 07:50:39: start model_add_line... INFO @ Tue, 16 Jun 2020 07:50:39: start X-correlation... INFO @ Tue, 16 Jun 2020 07:50:39: end of X-cor INFO @ Tue, 16 Jun 2020 07:50:39: #2 finished! INFO @ Tue, 16 Jun 2020 07:50:39: #2 predicted fragment length is 33 bps INFO @ Tue, 16 Jun 2020 07:50:39: #2 alternative fragment length(s) may be 4,33 bps INFO @ Tue, 16 Jun 2020 07:50:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX147642/SRX147642.05_model.r WARNING @ Tue, 16 Jun 2020 07:50:39: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:50:39: #2 You may need to consider one of the other alternative d(s): 4,33 WARNING @ Tue, 16 Jun 2020 07:50:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 07:50:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:50:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:50:48: #3 Call peaks for each chromosome... 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, 16 Jun 2020 07:50:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX147642/SRX147642.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX147642/SRX147642.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX147642/SRX147642.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX147642/SRX147642.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, 16 Jun 2020 07:50:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:50:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:50:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX147642/SRX147642.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:50:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX147642/SRX147642.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:50:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX147642/SRX147642.05_summits.bed INFO @ Tue, 16 Jun 2020 07:50:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (432 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:50:56: 1000000 INFO @ Tue, 16 Jun 2020 07:51:01: 2000000 INFO @ Tue, 16 Jun 2020 07:51:06: 3000000 INFO @ Tue, 16 Jun 2020 07:51:09: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:51:09: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:51:09: #1 total tags in treatment: 3630927 INFO @ Tue, 16 Jun 2020 07:51:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:51:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:51:09: #1 tags after filtering in treatment: 3630927 INFO @ Tue, 16 Jun 2020 07:51:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:51:09: #1 finished! INFO @ Tue, 16 Jun 2020 07:51:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:51:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:51:10: #2 number of paired peaks: 469 WARNING @ Tue, 16 Jun 2020 07:51:10: Fewer paired peaks (469) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 469 pairs to build model! INFO @ Tue, 16 Jun 2020 07:51:10: start model_add_line... INFO @ Tue, 16 Jun 2020 07:51:10: start X-correlation... INFO @ Tue, 16 Jun 2020 07:51:10: end of X-cor INFO @ Tue, 16 Jun 2020 07:51:10: #2 finished! INFO @ Tue, 16 Jun 2020 07:51:10: #2 predicted fragment length is 33 bps INFO @ Tue, 16 Jun 2020 07:51:10: #2 alternative fragment length(s) may be 4,33 bps INFO @ Tue, 16 Jun 2020 07:51:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX147642/SRX147642.10_model.r WARNING @ Tue, 16 Jun 2020 07:51:10: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:51:10: #2 You may need to consider one of the other alternative d(s): 4,33 WARNING @ Tue, 16 Jun 2020 07:51:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 07:51:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:51:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:51:18: #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, 16 Jun 2020 07:51:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX147642/SRX147642.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX147642/SRX147642.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX147642/SRX147642.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX147642/SRX147642.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, 16 Jun 2020 07:51:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:51:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:51:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX147642/SRX147642.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:51:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX147642/SRX147642.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:51:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX147642/SRX147642.10_summits.bed INFO @ Tue, 16 Jun 2020 07:51:22: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (220 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:51:26: 1000000 INFO @ Tue, 16 Jun 2020 07:51:31: 2000000 INFO @ Tue, 16 Jun 2020 07:51:36: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:51:39: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:51:39: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:51:39: #1 total tags in treatment: 3630927 INFO @ Tue, 16 Jun 2020 07:51:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:51:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:51:39: #1 tags after filtering in treatment: 3630927 INFO @ Tue, 16 Jun 2020 07:51:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:51:39: #1 finished! INFO @ Tue, 16 Jun 2020 07:51:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:51:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:51:40: #2 number of paired peaks: 469 WARNING @ Tue, 16 Jun 2020 07:51:40: Fewer paired peaks (469) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 469 pairs to build model! INFO @ Tue, 16 Jun 2020 07:51:40: start model_add_line... INFO @ Tue, 16 Jun 2020 07:51:40: start X-correlation... INFO @ Tue, 16 Jun 2020 07:51:40: end of X-cor INFO @ Tue, 16 Jun 2020 07:51:40: #2 finished! INFO @ Tue, 16 Jun 2020 07:51:40: #2 predicted fragment length is 33 bps INFO @ Tue, 16 Jun 2020 07:51:40: #2 alternative fragment length(s) may be 4,33 bps INFO @ Tue, 16 Jun 2020 07:51:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX147642/SRX147642.20_model.r WARNING @ Tue, 16 Jun 2020 07:51:40: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:51:40: #2 You may need to consider one of the other alternative d(s): 4,33 WARNING @ Tue, 16 Jun 2020 07:51:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 07:51:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:51:40: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:51:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:51:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX147642/SRX147642.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:51:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX147642/SRX147642.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:51:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX147642/SRX147642.20_summits.bed INFO @ Tue, 16 Jun 2020 07:51:52: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (61 records, 4 fields): 1 millis CompletedMACS2peakCalling