Job ID = 6367596 SRX = SRX331353 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:29:51 prefetch.2.10.7: 1) Downloading 'SRR947590'... 2020-06-15T23:29:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:33:32 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:33:32 prefetch.2.10.7: 1) 'SRR947590' was downloaded successfully Read 13809537 spots for SRR947590/SRR947590.sra Written 13809537 spots for SRR947590/SRR947590.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: 00:02:11 13809537 reads; of these: 13809537 (100.00%) were unpaired; of these: 2268835 (16.43%) aligned 0 times 9710160 (70.31%) aligned exactly 1 time 1830542 (13.26%) aligned >1 times 83.57% overall alignment rate Time searching: 00:02:11 Overall time: 00:02:11 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] 1987986 / 11540702 = 0.1723 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 08:39:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331353/SRX331353.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331353/SRX331353.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331353/SRX331353.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331353/SRX331353.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 08:39:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:39:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:39:22: 1000000 INFO @ Tue, 16 Jun 2020 08:39:28: 2000000 INFO @ Tue, 16 Jun 2020 08:39:33: 3000000 INFO @ Tue, 16 Jun 2020 08:39:39: 4000000 INFO @ Tue, 16 Jun 2020 08:39:44: 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 08:39:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331353/SRX331353.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331353/SRX331353.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331353/SRX331353.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331353/SRX331353.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 08:39:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:39:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:39:50: 6000000 INFO @ Tue, 16 Jun 2020 08:39:52: 1000000 INFO @ Tue, 16 Jun 2020 08:39:55: 7000000 INFO @ Tue, 16 Jun 2020 08:39:58: 2000000 INFO @ Tue, 16 Jun 2020 08:40:01: 8000000 INFO @ Tue, 16 Jun 2020 08:40:04: 3000000 INFO @ Tue, 16 Jun 2020 08:40:06: 9000000 INFO @ Tue, 16 Jun 2020 08:40:09: 4000000 INFO @ Tue, 16 Jun 2020 08:40:10: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:40:10: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:40:10: #1 total tags in treatment: 9552716 INFO @ Tue, 16 Jun 2020 08:40:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:40:10: #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 08:40:10: #1 tags after filtering in treatment: 9552716 INFO @ Tue, 16 Jun 2020 08:40:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:40:10: #1 finished! INFO @ Tue, 16 Jun 2020 08:40:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:40:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:40:10: #2 number of paired peaks: 277 WARNING @ Tue, 16 Jun 2020 08:40:10: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Tue, 16 Jun 2020 08:40:10: start model_add_line... INFO @ Tue, 16 Jun 2020 08:40:10: start X-correlation... INFO @ Tue, 16 Jun 2020 08:40:11: end of X-cor INFO @ Tue, 16 Jun 2020 08:40:11: #2 finished! INFO @ Tue, 16 Jun 2020 08:40:11: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 08:40:11: #2 alternative fragment length(s) may be 2,44,532,570 bps INFO @ Tue, 16 Jun 2020 08:40:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331353/SRX331353.05_model.r WARNING @ Tue, 16 Jun 2020 08:40:11: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:40:11: #2 You may need to consider one of the other alternative d(s): 2,44,532,570 WARNING @ Tue, 16 Jun 2020 08:40:11: #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 08:40:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:40:11: #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 08:40:15: 5000000 INFO @ Tue, 16 Jun 2020 08:40:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331353/SRX331353.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331353/SRX331353.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331353/SRX331353.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331353/SRX331353.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 08:40:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:40:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:40:21: 6000000 INFO @ Tue, 16 Jun 2020 08:40:22: 1000000 INFO @ Tue, 16 Jun 2020 08:40:27: 7000000 INFO @ Tue, 16 Jun 2020 08:40:27: 2000000 INFO @ Tue, 16 Jun 2020 08:40:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:40:32: 3000000 INFO @ Tue, 16 Jun 2020 08:40:32: 8000000 INFO @ Tue, 16 Jun 2020 08:40:37: 4000000 INFO @ Tue, 16 Jun 2020 08:40:38: 9000000 INFO @ Tue, 16 Jun 2020 08:40:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331353/SRX331353.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:40:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331353/SRX331353.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:40:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331353/SRX331353.05_summits.bed INFO @ Tue, 16 Jun 2020 08:40:38: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (580 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:40:41: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:40:41: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:40:41: #1 total tags in treatment: 9552716 INFO @ Tue, 16 Jun 2020 08:40:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:40:41: #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 08:40:41: #1 tags after filtering in treatment: 9552716 INFO @ Tue, 16 Jun 2020 08:40:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:40:41: #1 finished! INFO @ Tue, 16 Jun 2020 08:40:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:40:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:40:41: 5000000 INFO @ Tue, 16 Jun 2020 08:40:42: #2 number of paired peaks: 277 WARNING @ Tue, 16 Jun 2020 08:40:42: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Tue, 16 Jun 2020 08:40:42: start model_add_line... INFO @ Tue, 16 Jun 2020 08:40:42: start X-correlation... INFO @ Tue, 16 Jun 2020 08:40:42: end of X-cor INFO @ Tue, 16 Jun 2020 08:40:42: #2 finished! INFO @ Tue, 16 Jun 2020 08:40:42: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 08:40:42: #2 alternative fragment length(s) may be 2,44,532,570 bps INFO @ Tue, 16 Jun 2020 08:40:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331353/SRX331353.10_model.r WARNING @ Tue, 16 Jun 2020 08:40:42: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:40:42: #2 You may need to consider one of the other alternative d(s): 2,44,532,570 WARNING @ Tue, 16 Jun 2020 08:40:42: #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 08:40:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:40:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:40:46: 6000000 INFO @ Tue, 16 Jun 2020 08:40:51: 7000000 INFO @ Tue, 16 Jun 2020 08:40:56: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:41:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:41:01: 9000000 INFO @ Tue, 16 Jun 2020 08:41:03: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:41:03: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:41:03: #1 total tags in treatment: 9552716 INFO @ Tue, 16 Jun 2020 08:41:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:41:03: #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 08:41:04: #1 tags after filtering in treatment: 9552716 INFO @ Tue, 16 Jun 2020 08:41:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:41:04: #1 finished! INFO @ Tue, 16 Jun 2020 08:41:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:41:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:41:04: #2 number of paired peaks: 277 WARNING @ Tue, 16 Jun 2020 08:41:04: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Tue, 16 Jun 2020 08:41:04: start model_add_line... INFO @ Tue, 16 Jun 2020 08:41:04: start X-correlation... INFO @ Tue, 16 Jun 2020 08:41:04: end of X-cor INFO @ Tue, 16 Jun 2020 08:41:04: #2 finished! INFO @ Tue, 16 Jun 2020 08:41:04: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 08:41:04: #2 alternative fragment length(s) may be 2,44,532,570 bps INFO @ Tue, 16 Jun 2020 08:41:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331353/SRX331353.20_model.r WARNING @ Tue, 16 Jun 2020 08:41:04: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:41:04: #2 You may need to consider one of the other alternative d(s): 2,44,532,570 WARNING @ Tue, 16 Jun 2020 08:41:04: #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 08:41:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:41:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:41:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331353/SRX331353.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:41:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331353/SRX331353.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:41:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331353/SRX331353.10_summits.bed INFO @ Tue, 16 Jun 2020 08:41:09: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (303 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:41:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:41:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331353/SRX331353.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:41:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331353/SRX331353.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:41:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331353/SRX331353.20_summits.bed INFO @ Tue, 16 Jun 2020 08:41:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (119 records, 4 fields): 1 millis CompletedMACS2peakCalling