Job ID = 6367655 SRX = SRX373277 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:31:50 prefetch.2.10.7: 1) Downloading 'SRR1024195'... 2020-06-15T23:31:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:35:26 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:35:26 prefetch.2.10.7: 1) 'SRR1024195' was downloaded successfully Read 19946188 spots for SRR1024195/SRR1024195.sra Written 19946188 spots for SRR1024195/SRR1024195.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: 00:02:32 19946188 reads; of these: 19946188 (100.00%) were unpaired; of these: 14221767 (71.30%) aligned 0 times 4705768 (23.59%) aligned exactly 1 time 1018653 (5.11%) aligned >1 times 28.70% overall alignment rate Time searching: 00:02:32 Overall time: 00:02:32 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] 649246 / 5724421 = 0.1134 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 08:40:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX373277/SRX373277.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX373277/SRX373277.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX373277/SRX373277.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX373277/SRX373277.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 08:40:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:40:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:40:55: 1000000 INFO @ Tue, 16 Jun 2020 08:41:01: 2000000 INFO @ Tue, 16 Jun 2020 08:41:06: 3000000 INFO @ Tue, 16 Jun 2020 08:41:12: 4000000 INFO @ Tue, 16 Jun 2020 08:41:17: 5000000 INFO @ Tue, 16 Jun 2020 08:41:17: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:41:17: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:41:17: #1 total tags in treatment: 5075175 INFO @ Tue, 16 Jun 2020 08:41:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:41:17: #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 08:41:17: #1 tags after filtering in treatment: 5075175 INFO @ Tue, 16 Jun 2020 08:41:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:41:17: #1 finished! INFO @ Tue, 16 Jun 2020 08:41:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:41:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:41:18: #2 number of paired peaks: 406 WARNING @ Tue, 16 Jun 2020 08:41:18: Fewer paired peaks (406) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 406 pairs to build model! INFO @ Tue, 16 Jun 2020 08:41:18: start model_add_line... INFO @ Tue, 16 Jun 2020 08:41:18: start X-correlation... INFO @ Tue, 16 Jun 2020 08:41:18: end of X-cor INFO @ Tue, 16 Jun 2020 08:41:18: #2 finished! INFO @ Tue, 16 Jun 2020 08:41:18: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 08:41:18: #2 alternative fragment length(s) may be 51 bps INFO @ Tue, 16 Jun 2020 08:41:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX373277/SRX373277.05_model.r WARNING @ Tue, 16 Jun 2020 08:41:18: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:41:18: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Tue, 16 Jun 2020 08:41:18: #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 08:41:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:41:18: #3 Pre-compute pvalue-qvalue table... 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 08:41:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX373277/SRX373277.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX373277/SRX373277.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX373277/SRX373277.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX373277/SRX373277.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 08:41:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:41:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:41:25: 1000000 INFO @ Tue, 16 Jun 2020 08:41:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:41:31: 2000000 INFO @ Tue, 16 Jun 2020 08:41:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX373277/SRX373277.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:41:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX373277/SRX373277.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:41:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX373277/SRX373277.05_summits.bed INFO @ Tue, 16 Jun 2020 08:41:35: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (484 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:41:36: 3000000 INFO @ Tue, 16 Jun 2020 08:41:41: 4000000 INFO @ Tue, 16 Jun 2020 08:41:47: 5000000 INFO @ Tue, 16 Jun 2020 08:41:47: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:41:47: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:41:47: #1 total tags in treatment: 5075175 INFO @ Tue, 16 Jun 2020 08:41:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:41:47: #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 08:41:47: #1 tags after filtering in treatment: 5075175 INFO @ Tue, 16 Jun 2020 08:41:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:41:47: #1 finished! INFO @ Tue, 16 Jun 2020 08:41:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:41:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:41:48: #2 number of paired peaks: 406 WARNING @ Tue, 16 Jun 2020 08:41:48: Fewer paired peaks (406) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 406 pairs to build model! INFO @ Tue, 16 Jun 2020 08:41:48: start model_add_line... INFO @ Tue, 16 Jun 2020 08:41:48: start X-correlation... INFO @ Tue, 16 Jun 2020 08:41:48: end of X-cor INFO @ Tue, 16 Jun 2020 08:41:48: #2 finished! INFO @ Tue, 16 Jun 2020 08:41:48: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 08:41:48: #2 alternative fragment length(s) may be 51 bps INFO @ Tue, 16 Jun 2020 08:41:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX373277/SRX373277.10_model.r WARNING @ Tue, 16 Jun 2020 08:41:48: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:41:48: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Tue, 16 Jun 2020 08:41:48: #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 08:41:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:41:48: #3 Pre-compute pvalue-qvalue table... 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 08:41:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX373277/SRX373277.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX373277/SRX373277.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX373277/SRX373277.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX373277/SRX373277.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 08:41:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:41:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:41:56: 1000000 INFO @ Tue, 16 Jun 2020 08:41:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:42:02: 2000000 INFO @ Tue, 16 Jun 2020 08:42:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX373277/SRX373277.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:42:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX373277/SRX373277.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:42:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX373277/SRX373277.10_summits.bed INFO @ Tue, 16 Jun 2020 08:42:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (287 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:42:08: 3000000 INFO @ Tue, 16 Jun 2020 08:42:14: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:42:20: 5000000 INFO @ Tue, 16 Jun 2020 08:42:21: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:42:21: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:42:21: #1 total tags in treatment: 5075175 INFO @ Tue, 16 Jun 2020 08:42:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:42:21: #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 08:42:21: #1 tags after filtering in treatment: 5075175 INFO @ Tue, 16 Jun 2020 08:42:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:42:21: #1 finished! INFO @ Tue, 16 Jun 2020 08:42:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:42:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:42:21: #2 number of paired peaks: 406 WARNING @ Tue, 16 Jun 2020 08:42:21: Fewer paired peaks (406) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 406 pairs to build model! INFO @ Tue, 16 Jun 2020 08:42:21: start model_add_line... INFO @ Tue, 16 Jun 2020 08:42:21: start X-correlation... INFO @ Tue, 16 Jun 2020 08:42:21: end of X-cor INFO @ Tue, 16 Jun 2020 08:42:21: #2 finished! INFO @ Tue, 16 Jun 2020 08:42:21: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 08:42:21: #2 alternative fragment length(s) may be 51 bps INFO @ Tue, 16 Jun 2020 08:42:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX373277/SRX373277.20_model.r WARNING @ Tue, 16 Jun 2020 08:42:21: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:42:21: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Tue, 16 Jun 2020 08:42:21: #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 08:42:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:42:21: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:42:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:42:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX373277/SRX373277.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:42:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX373277/SRX373277.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:42:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX373277/SRX373277.20_summits.bed INFO @ Tue, 16 Jun 2020 08:42:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (136 records, 4 fields): 1 millis CompletedMACS2peakCalling