Job ID = 6366303 SRX = SRX1078727 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:57:23 prefetch.2.10.7: 1) Downloading 'SRR2084334'... 2020-06-15T22:57:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:59:14 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:59:14 prefetch.2.10.7: 1) 'SRR2084334' was downloaded successfully Read 28631131 spots for SRR2084334/SRR2084334.sra Written 28631131 spots for SRR2084334/SRR2084334.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: 00:05:36 28631131 reads; of these: 28631131 (100.00%) were unpaired; of these: 11926469 (41.66%) aligned 0 times 13953348 (48.73%) aligned exactly 1 time 2751314 (9.61%) aligned >1 times 58.34% overall alignment rate Time searching: 00:05:36 Overall time: 00:05:36 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] 12865403 / 16704662 = 0.7702 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 08:10:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078727/SRX1078727.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078727/SRX1078727.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078727/SRX1078727.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078727/SRX1078727.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 08:10:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:10:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:10:42: 1000000 INFO @ Tue, 16 Jun 2020 08:10:50: 2000000 INFO @ Tue, 16 Jun 2020 08:10:58: 3000000 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 08:11:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078727/SRX1078727.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078727/SRX1078727.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078727/SRX1078727.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078727/SRX1078727.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 08:11:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:11:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:11:05: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:11:05: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:11:05: #1 total tags in treatment: 3839259 INFO @ Tue, 16 Jun 2020 08:11:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:11:05: #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 08:11:05: #1 tags after filtering in treatment: 3839259 INFO @ Tue, 16 Jun 2020 08:11:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:11:05: #1 finished! INFO @ Tue, 16 Jun 2020 08:11:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:11:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:11:06: #2 number of paired peaks: 884 WARNING @ Tue, 16 Jun 2020 08:11:06: Fewer paired peaks (884) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 884 pairs to build model! INFO @ Tue, 16 Jun 2020 08:11:06: start model_add_line... INFO @ Tue, 16 Jun 2020 08:11:06: start X-correlation... INFO @ Tue, 16 Jun 2020 08:11:06: end of X-cor INFO @ Tue, 16 Jun 2020 08:11:06: #2 finished! INFO @ Tue, 16 Jun 2020 08:11:06: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 08:11:06: #2 alternative fragment length(s) may be 4,47 bps INFO @ Tue, 16 Jun 2020 08:11:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078727/SRX1078727.05_model.r WARNING @ Tue, 16 Jun 2020 08:11:06: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:11:06: #2 You may need to consider one of the other alternative d(s): 4,47 WARNING @ Tue, 16 Jun 2020 08:11:06: #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 08:11:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:11:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:11:11: 1000000 INFO @ Tue, 16 Jun 2020 08:11:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:11:16: 2000000 INFO @ Tue, 16 Jun 2020 08:11:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1078727/SRX1078727.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:11:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1078727/SRX1078727.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:11:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1078727/SRX1078727.05_summits.bed INFO @ Tue, 16 Jun 2020 08:11:18: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (840 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:11:22: 3000000 INFO @ Tue, 16 Jun 2020 08:11:27: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:11:27: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:11:27: #1 total tags in treatment: 3839259 INFO @ Tue, 16 Jun 2020 08:11:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:11:27: #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 08:11:27: #1 tags after filtering in treatment: 3839259 INFO @ Tue, 16 Jun 2020 08:11:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:11:27: #1 finished! INFO @ Tue, 16 Jun 2020 08:11:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:11:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:11:28: #2 number of paired peaks: 884 WARNING @ Tue, 16 Jun 2020 08:11:28: Fewer paired peaks (884) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 884 pairs to build model! INFO @ Tue, 16 Jun 2020 08:11:28: start model_add_line... INFO @ Tue, 16 Jun 2020 08:11:28: start X-correlation... INFO @ Tue, 16 Jun 2020 08:11:28: end of X-cor INFO @ Tue, 16 Jun 2020 08:11:28: #2 finished! INFO @ Tue, 16 Jun 2020 08:11:28: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 08:11:28: #2 alternative fragment length(s) may be 4,47 bps INFO @ Tue, 16 Jun 2020 08:11:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078727/SRX1078727.10_model.r WARNING @ Tue, 16 Jun 2020 08:11:28: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:11:28: #2 You may need to consider one of the other alternative d(s): 4,47 WARNING @ Tue, 16 Jun 2020 08:11:28: #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 08:11:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:11:28: #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 08:11:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078727/SRX1078727.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078727/SRX1078727.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078727/SRX1078727.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078727/SRX1078727.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 08:11:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:11:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:11:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:11:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1078727/SRX1078727.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:11:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1078727/SRX1078727.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:11:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1078727/SRX1078727.10_summits.bed INFO @ Tue, 16 Jun 2020 08:11:40: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (583 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:11:42: 1000000 INFO @ Tue, 16 Jun 2020 08:11:50: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:11:59: 3000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:12:06: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:12:06: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:12:06: #1 total tags in treatment: 3839259 INFO @ Tue, 16 Jun 2020 08:12:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:12:06: #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 08:12:06: #1 tags after filtering in treatment: 3839259 INFO @ Tue, 16 Jun 2020 08:12:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:12:06: #1 finished! INFO @ Tue, 16 Jun 2020 08:12:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:12:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:12:06: #2 number of paired peaks: 884 WARNING @ Tue, 16 Jun 2020 08:12:06: Fewer paired peaks (884) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 884 pairs to build model! INFO @ Tue, 16 Jun 2020 08:12:06: start model_add_line... INFO @ Tue, 16 Jun 2020 08:12:06: start X-correlation... INFO @ Tue, 16 Jun 2020 08:12:06: end of X-cor INFO @ Tue, 16 Jun 2020 08:12:06: #2 finished! INFO @ Tue, 16 Jun 2020 08:12:06: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 08:12:06: #2 alternative fragment length(s) may be 4,47 bps INFO @ Tue, 16 Jun 2020 08:12:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078727/SRX1078727.20_model.r WARNING @ Tue, 16 Jun 2020 08:12:06: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:12:06: #2 You may need to consider one of the other alternative d(s): 4,47 WARNING @ Tue, 16 Jun 2020 08:12:06: #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 08:12:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:12:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:12:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:12:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1078727/SRX1078727.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:12:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1078727/SRX1078727.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:12:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1078727/SRX1078727.20_summits.bed INFO @ Tue, 16 Jun 2020 08:12:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (264 records, 4 fields): 1 millis CompletedMACS2peakCalling