Job ID = 6367692 SRX = SRX3942555 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:32:20 prefetch.2.10.7: 1) Downloading 'SRR7010076'... 2020-06-15T23:32:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:35:40 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:35:40 prefetch.2.10.7: 1) 'SRR7010076' was downloaded successfully 2020-06-15T23:35:40 prefetch.2.10.7: 'SRR7010076' has 0 unresolved dependencies Read 21320060 spots for SRR7010076/SRR7010076.sra Written 21320060 spots for SRR7010076/SRR7010076.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: 00:06:50 21320060 reads; of these: 21320060 (100.00%) were unpaired; of these: 6002431 (28.15%) aligned 0 times 11425453 (53.59%) aligned exactly 1 time 3892176 (18.26%) aligned >1 times 71.85% overall alignment rate Time searching: 00:06:50 Overall time: 00:06:50 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] 10506436 / 15317629 = 0.6859 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 08:47:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3942555/SRX3942555.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3942555/SRX3942555.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3942555/SRX3942555.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3942555/SRX3942555.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 08:47:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:47:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:47:09: 1000000 INFO @ Tue, 16 Jun 2020 08:47:15: 2000000 INFO @ Tue, 16 Jun 2020 08:47:20: 3000000 INFO @ Tue, 16 Jun 2020 08:47:26: 4000000 INFO @ Tue, 16 Jun 2020 08:47:30: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:47:30: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:47:30: #1 total tags in treatment: 4811193 INFO @ Tue, 16 Jun 2020 08:47:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:47:30: #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 08:47:30: #1 tags after filtering in treatment: 4811193 INFO @ Tue, 16 Jun 2020 08:47:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:47:30: #1 finished! INFO @ Tue, 16 Jun 2020 08:47:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:47:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:47:31: #2 number of paired peaks: 2624 INFO @ Tue, 16 Jun 2020 08:47:31: start model_add_line... INFO @ Tue, 16 Jun 2020 08:47:31: start X-correlation... INFO @ Tue, 16 Jun 2020 08:47:31: end of X-cor INFO @ Tue, 16 Jun 2020 08:47:31: #2 finished! INFO @ Tue, 16 Jun 2020 08:47:31: #2 predicted fragment length is 85 bps INFO @ Tue, 16 Jun 2020 08:47:31: #2 alternative fragment length(s) may be 3,85,88,598 bps INFO @ Tue, 16 Jun 2020 08:47:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3942555/SRX3942555.05_model.r WARNING @ Tue, 16 Jun 2020 08:47:31: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:47:31: #2 You may need to consider one of the other alternative d(s): 3,85,88,598 WARNING @ Tue, 16 Jun 2020 08:47:31: #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 08:47:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:47:31: #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 08:47:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3942555/SRX3942555.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3942555/SRX3942555.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3942555/SRX3942555.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3942555/SRX3942555.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 08:47:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:47:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:47:40: 1000000 INFO @ Tue, 16 Jun 2020 08:47:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:47:45: 2000000 INFO @ Tue, 16 Jun 2020 08:47:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3942555/SRX3942555.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:47:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3942555/SRX3942555.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:47:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3942555/SRX3942555.05_summits.bed INFO @ Tue, 16 Jun 2020 08:47:48: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1392 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:47:51: 3000000 INFO @ Tue, 16 Jun 2020 08:47:57: 4000000 INFO @ Tue, 16 Jun 2020 08:48:01: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:48:01: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:48:01: #1 total tags in treatment: 4811193 INFO @ Tue, 16 Jun 2020 08:48:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:48:01: #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 08:48:01: #1 tags after filtering in treatment: 4811193 INFO @ Tue, 16 Jun 2020 08:48:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:48:01: #1 finished! INFO @ Tue, 16 Jun 2020 08:48:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:48:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:48:02: #2 number of paired peaks: 2624 INFO @ Tue, 16 Jun 2020 08:48:02: start model_add_line... INFO @ Tue, 16 Jun 2020 08:48:02: start X-correlation... INFO @ Tue, 16 Jun 2020 08:48:02: end of X-cor INFO @ Tue, 16 Jun 2020 08:48:02: #2 finished! INFO @ Tue, 16 Jun 2020 08:48:02: #2 predicted fragment length is 85 bps INFO @ Tue, 16 Jun 2020 08:48:02: #2 alternative fragment length(s) may be 3,85,88,598 bps INFO @ Tue, 16 Jun 2020 08:48:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3942555/SRX3942555.10_model.r WARNING @ Tue, 16 Jun 2020 08:48:02: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:48:02: #2 You may need to consider one of the other alternative d(s): 3,85,88,598 WARNING @ Tue, 16 Jun 2020 08:48:02: #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 08:48:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:48:02: #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 08:48:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3942555/SRX3942555.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3942555/SRX3942555.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3942555/SRX3942555.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3942555/SRX3942555.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 08:48:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:48:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:48:10: 1000000 INFO @ Tue, 16 Jun 2020 08:48:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:48:16: 2000000 INFO @ Tue, 16 Jun 2020 08:48:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3942555/SRX3942555.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:48:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3942555/SRX3942555.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:48:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3942555/SRX3942555.10_summits.bed INFO @ Tue, 16 Jun 2020 08:48:20: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (698 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:48:22: 3000000 INFO @ Tue, 16 Jun 2020 08:48:28: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:48:33: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:48:33: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:48:33: #1 total tags in treatment: 4811193 INFO @ Tue, 16 Jun 2020 08:48:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:48:33: #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 08:48:33: #1 tags after filtering in treatment: 4811193 INFO @ Tue, 16 Jun 2020 08:48:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:48:33: #1 finished! INFO @ Tue, 16 Jun 2020 08:48:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:48:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:48:33: #2 number of paired peaks: 2624 INFO @ Tue, 16 Jun 2020 08:48:33: start model_add_line... INFO @ Tue, 16 Jun 2020 08:48:33: start X-correlation... INFO @ Tue, 16 Jun 2020 08:48:33: end of X-cor INFO @ Tue, 16 Jun 2020 08:48:33: #2 finished! INFO @ Tue, 16 Jun 2020 08:48:33: #2 predicted fragment length is 85 bps INFO @ Tue, 16 Jun 2020 08:48:33: #2 alternative fragment length(s) may be 3,85,88,598 bps INFO @ Tue, 16 Jun 2020 08:48:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3942555/SRX3942555.20_model.r WARNING @ Tue, 16 Jun 2020 08:48:33: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:48:33: #2 You may need to consider one of the other alternative d(s): 3,85,88,598 WARNING @ Tue, 16 Jun 2020 08:48:33: #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 08:48:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:48:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:48:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:48:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3942555/SRX3942555.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:48:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3942555/SRX3942555.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:48:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3942555/SRX3942555.20_summits.bed INFO @ Tue, 16 Jun 2020 08:48:52: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (299 records, 4 fields): 1 millis CompletedMACS2peakCalling