Job ID = 6367732 SRX = SRX4082346 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:34:35 prefetch.2.10.7: 1) Downloading 'SRR7164164'... 2020-06-15T23:34:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:36:02 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:36:03 prefetch.2.10.7: 'SRR7164164' is valid 2020-06-15T23:36:03 prefetch.2.10.7: 1) 'SRR7164164' was downloaded successfully 2020-06-15T23:36:03 prefetch.2.10.7: 'SRR7164164' has 0 unresolved dependencies Read 12247529 spots for SRR7164164/SRR7164164.sra Written 12247529 spots for SRR7164164/SRR7164164.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: 00:02:43 12247529 reads; of these: 12247529 (100.00%) were unpaired; of these: 291294 (2.38%) aligned 0 times 10484942 (85.61%) aligned exactly 1 time 1471293 (12.01%) aligned >1 times 97.62% overall alignment rate Time searching: 00:02:43 Overall time: 00:02:43 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_sort_core] merging from 8 files... [bam_rmdupse_core] 5004244 / 11956235 = 0.4185 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 08:42:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082346/SRX4082346.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082346/SRX4082346.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082346/SRX4082346.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082346/SRX4082346.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 08:42:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:42:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:42:15: 1000000 INFO @ Tue, 16 Jun 2020 08:42:20: 2000000 INFO @ Tue, 16 Jun 2020 08:42:25: 3000000 INFO @ Tue, 16 Jun 2020 08:42:30: 4000000 INFO @ Tue, 16 Jun 2020 08:42:34: 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, 16 Jun 2020 08:42:39: 6000000 INFO @ Tue, 16 Jun 2020 08:42:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082346/SRX4082346.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082346/SRX4082346.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082346/SRX4082346.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082346/SRX4082346.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 08:42:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:42:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:42:44: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:42:44: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:42:44: #1 total tags in treatment: 6951991 INFO @ Tue, 16 Jun 2020 08:42:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:42:44: #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 08:42:44: #1 tags after filtering in treatment: 6951991 INFO @ Tue, 16 Jun 2020 08:42:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:42:44: #1 finished! INFO @ Tue, 16 Jun 2020 08:42:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:42:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:42:45: #2 number of paired peaks: 248 WARNING @ Tue, 16 Jun 2020 08:42:45: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Tue, 16 Jun 2020 08:42:45: start model_add_line... INFO @ Tue, 16 Jun 2020 08:42:45: start X-correlation... INFO @ Tue, 16 Jun 2020 08:42:45: end of X-cor INFO @ Tue, 16 Jun 2020 08:42:45: #2 finished! INFO @ Tue, 16 Jun 2020 08:42:45: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 08:42:45: #2 alternative fragment length(s) may be 3,52,598 bps INFO @ Tue, 16 Jun 2020 08:42:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082346/SRX4082346.05_model.r WARNING @ Tue, 16 Jun 2020 08:42:45: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:42:45: #2 You may need to consider one of the other alternative d(s): 3,52,598 WARNING @ Tue, 16 Jun 2020 08:42:45: #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 08:42:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:42:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:42:45: 1000000 INFO @ Tue, 16 Jun 2020 08:42:50: 2000000 INFO @ Tue, 16 Jun 2020 08:42:55: 3000000 INFO @ Tue, 16 Jun 2020 08:42:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:43:00: 4000000 INFO @ Tue, 16 Jun 2020 08:43:05: 5000000 INFO @ Tue, 16 Jun 2020 08:43:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082346/SRX4082346.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:43:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082346/SRX4082346.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:43:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082346/SRX4082346.05_summits.bed INFO @ Tue, 16 Jun 2020 08:43:06: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (681 records, 4 fields): 2 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, 16 Jun 2020 08:43:10: 6000000 INFO @ Tue, 16 Jun 2020 08:43:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082346/SRX4082346.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082346/SRX4082346.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082346/SRX4082346.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082346/SRX4082346.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 08:43:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:43:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:43:14: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:43:14: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:43:14: #1 total tags in treatment: 6951991 INFO @ Tue, 16 Jun 2020 08:43:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:43:14: #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 08:43:15: #1 tags after filtering in treatment: 6951991 INFO @ Tue, 16 Jun 2020 08:43:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:43:15: #1 finished! INFO @ Tue, 16 Jun 2020 08:43:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:43:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:43:15: #2 number of paired peaks: 248 WARNING @ Tue, 16 Jun 2020 08:43:15: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Tue, 16 Jun 2020 08:43:15: start model_add_line... INFO @ Tue, 16 Jun 2020 08:43:15: start X-correlation... INFO @ Tue, 16 Jun 2020 08:43:15: end of X-cor INFO @ Tue, 16 Jun 2020 08:43:15: #2 finished! INFO @ Tue, 16 Jun 2020 08:43:15: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 08:43:15: #2 alternative fragment length(s) may be 3,52,598 bps INFO @ Tue, 16 Jun 2020 08:43:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082346/SRX4082346.10_model.r WARNING @ Tue, 16 Jun 2020 08:43:15: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:43:15: #2 You may need to consider one of the other alternative d(s): 3,52,598 WARNING @ Tue, 16 Jun 2020 08:43:15: #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 08:43:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:43:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:43:15: 1000000 INFO @ Tue, 16 Jun 2020 08:43:20: 2000000 INFO @ Tue, 16 Jun 2020 08:43:25: 3000000 INFO @ Tue, 16 Jun 2020 08:43:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:43:29: 4000000 INFO @ Tue, 16 Jun 2020 08:43:34: 5000000 INFO @ Tue, 16 Jun 2020 08:43:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082346/SRX4082346.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:43:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082346/SRX4082346.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:43:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082346/SRX4082346.10_summits.bed INFO @ Tue, 16 Jun 2020 08:43:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (189 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:43:39: 6000000 INFO @ Tue, 16 Jun 2020 08:43:43: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:43:43: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:43:43: #1 total tags in treatment: 6951991 INFO @ Tue, 16 Jun 2020 08:43:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:43:43: #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 08:43:43: #1 tags after filtering in treatment: 6951991 INFO @ Tue, 16 Jun 2020 08:43:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:43:43: #1 finished! INFO @ Tue, 16 Jun 2020 08:43:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:43:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:43:44: #2 number of paired peaks: 248 WARNING @ Tue, 16 Jun 2020 08:43:44: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Tue, 16 Jun 2020 08:43:44: start model_add_line... INFO @ Tue, 16 Jun 2020 08:43:44: start X-correlation... INFO @ Tue, 16 Jun 2020 08:43:44: end of X-cor INFO @ Tue, 16 Jun 2020 08:43:44: #2 finished! INFO @ Tue, 16 Jun 2020 08:43:44: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 08:43:44: #2 alternative fragment length(s) may be 3,52,598 bps INFO @ Tue, 16 Jun 2020 08:43:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082346/SRX4082346.20_model.r WARNING @ Tue, 16 Jun 2020 08:43:44: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:43:44: #2 You may need to consider one of the other alternative d(s): 3,52,598 WARNING @ Tue, 16 Jun 2020 08:43:44: #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 08:43:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:43:44: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:43:57: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:44:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082346/SRX4082346.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:44:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082346/SRX4082346.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:44:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082346/SRX4082346.20_summits.bed INFO @ Tue, 16 Jun 2020 08:44:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (73 records, 4 fields): 2 millis CompletedMACS2peakCalling