Job ID = 6367760 SRX = SRX4082374 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:39:59 prefetch.2.10.7: 1) Downloading 'SRR7164192'... 2020-06-15T23:39:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:41:26 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:41:26 prefetch.2.10.7: 'SRR7164192' is valid 2020-06-15T23:41:26 prefetch.2.10.7: 1) 'SRR7164192' was downloaded successfully 2020-06-15T23:41:26 prefetch.2.10.7: 'SRR7164192' has 0 unresolved dependencies Read 11738901 spots for SRR7164192/SRR7164192.sra Written 11738901 spots for SRR7164192/SRR7164192.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: 00:02:28 11738901 reads; of these: 11738901 (100.00%) were unpaired; of these: 1110908 (9.46%) aligned 0 times 8074908 (68.79%) aligned exactly 1 time 2553085 (21.75%) aligned >1 times 90.54% overall alignment rate Time searching: 00:02:28 Overall time: 00:02:28 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_sort_core] merging from 8 files... [bam_rmdupse_core] 1706374 / 10627993 = 0.1606 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 08:48:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082374/SRX4082374.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082374/SRX4082374.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082374/SRX4082374.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082374/SRX4082374.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 08:48:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:48:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:48:13: 1000000 INFO @ Tue, 16 Jun 2020 08:48:18: 2000000 INFO @ Tue, 16 Jun 2020 08:48:24: 3000000 INFO @ Tue, 16 Jun 2020 08:48:30: 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, 16 Jun 2020 08:48:35: 5000000 INFO @ Tue, 16 Jun 2020 08:48:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082374/SRX4082374.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082374/SRX4082374.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082374/SRX4082374.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082374/SRX4082374.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 08:48:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:48:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:48:41: 6000000 INFO @ Tue, 16 Jun 2020 08:48:43: 1000000 INFO @ Tue, 16 Jun 2020 08:48:47: 7000000 INFO @ Tue, 16 Jun 2020 08:48:49: 2000000 INFO @ Tue, 16 Jun 2020 08:48:54: 8000000 INFO @ Tue, 16 Jun 2020 08:48:56: 3000000 INFO @ Tue, 16 Jun 2020 08:48:59: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:48:59: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:48:59: #1 total tags in treatment: 8921619 INFO @ Tue, 16 Jun 2020 08:48:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:48:59: #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 08:49:00: #1 tags after filtering in treatment: 8921619 INFO @ Tue, 16 Jun 2020 08:49:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:49:00: #1 finished! INFO @ Tue, 16 Jun 2020 08:49:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:49:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:49:00: #2 number of paired peaks: 460 WARNING @ Tue, 16 Jun 2020 08:49:00: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Tue, 16 Jun 2020 08:49:00: start model_add_line... INFO @ Tue, 16 Jun 2020 08:49:00: start X-correlation... INFO @ Tue, 16 Jun 2020 08:49:00: end of X-cor INFO @ Tue, 16 Jun 2020 08:49:00: #2 finished! INFO @ Tue, 16 Jun 2020 08:49:00: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 08:49:00: #2 alternative fragment length(s) may be 3,48 bps INFO @ Tue, 16 Jun 2020 08:49:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082374/SRX4082374.05_model.r WARNING @ Tue, 16 Jun 2020 08:49:00: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:49:00: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Tue, 16 Jun 2020 08:49:00: #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 08:49:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:49:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:49:02: 4000000 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 08:49:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082374/SRX4082374.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082374/SRX4082374.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082374/SRX4082374.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082374/SRX4082374.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 08:49:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:49:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:49:07: 5000000 INFO @ Tue, 16 Jun 2020 08:49:13: 1000000 INFO @ Tue, 16 Jun 2020 08:49:13: 6000000 INFO @ Tue, 16 Jun 2020 08:49:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:49:18: 2000000 INFO @ Tue, 16 Jun 2020 08:49:19: 7000000 INFO @ Tue, 16 Jun 2020 08:49:24: 3000000 INFO @ Tue, 16 Jun 2020 08:49:24: 8000000 INFO @ Tue, 16 Jun 2020 08:49:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082374/SRX4082374.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:49:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082374/SRX4082374.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:49:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082374/SRX4082374.05_summits.bed INFO @ Tue, 16 Jun 2020 08:49:26: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (781 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:49:29: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:49:29: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:49:29: #1 total tags in treatment: 8921619 INFO @ Tue, 16 Jun 2020 08:49:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:49:29: #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 08:49:30: #1 tags after filtering in treatment: 8921619 INFO @ Tue, 16 Jun 2020 08:49:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:49:30: #1 finished! INFO @ Tue, 16 Jun 2020 08:49:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:49:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:49:30: 4000000 INFO @ Tue, 16 Jun 2020 08:49:30: #2 number of paired peaks: 460 WARNING @ Tue, 16 Jun 2020 08:49:30: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Tue, 16 Jun 2020 08:49:30: start model_add_line... INFO @ Tue, 16 Jun 2020 08:49:30: start X-correlation... INFO @ Tue, 16 Jun 2020 08:49:30: end of X-cor INFO @ Tue, 16 Jun 2020 08:49:30: #2 finished! INFO @ Tue, 16 Jun 2020 08:49:30: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 08:49:30: #2 alternative fragment length(s) may be 3,48 bps INFO @ Tue, 16 Jun 2020 08:49:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082374/SRX4082374.10_model.r WARNING @ Tue, 16 Jun 2020 08:49:30: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:49:30: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Tue, 16 Jun 2020 08:49:30: #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 08:49:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:49:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:49:35: 5000000 INFO @ Tue, 16 Jun 2020 08:49:41: 6000000 INFO @ Tue, 16 Jun 2020 08:49:46: 7000000 INFO @ Tue, 16 Jun 2020 08:49:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:49:51: 8000000 INFO @ Tue, 16 Jun 2020 08:49:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082374/SRX4082374.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:49:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082374/SRX4082374.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:49:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082374/SRX4082374.10_summits.bed INFO @ Tue, 16 Jun 2020 08:49:55: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (422 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:49:56: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:49:56: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:49:56: #1 total tags in treatment: 8921619 INFO @ Tue, 16 Jun 2020 08:49:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:49:56: #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 08:49:57: #1 tags after filtering in treatment: 8921619 INFO @ Tue, 16 Jun 2020 08:49:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:49:57: #1 finished! INFO @ Tue, 16 Jun 2020 08:49:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:49:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:49:57: #2 number of paired peaks: 460 WARNING @ Tue, 16 Jun 2020 08:49:57: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Tue, 16 Jun 2020 08:49:57: start model_add_line... INFO @ Tue, 16 Jun 2020 08:49:57: start X-correlation... INFO @ Tue, 16 Jun 2020 08:49:57: end of X-cor INFO @ Tue, 16 Jun 2020 08:49:57: #2 finished! INFO @ Tue, 16 Jun 2020 08:49:57: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 08:49:57: #2 alternative fragment length(s) may be 3,48 bps INFO @ Tue, 16 Jun 2020 08:49:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082374/SRX4082374.20_model.r WARNING @ Tue, 16 Jun 2020 08:49:57: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:49:57: #2 You may need to consider one of the other alternative d(s): 3,48 WARNING @ Tue, 16 Jun 2020 08:49:57: #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 08:49:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:49:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:50:14: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:50:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082374/SRX4082374.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:50:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082374/SRX4082374.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:50:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082374/SRX4082374.20_summits.bed INFO @ Tue, 16 Jun 2020 08:50:22: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (171 records, 4 fields): 2 millis CompletedMACS2peakCalling