Job ID = 6368772 SRX = SRX554724 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:24:18 prefetch.2.10.7: 1) Downloading 'SRR1301072'... 2020-06-16T00:24:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:25:29 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:25:29 prefetch.2.10.7: 'SRR1301072' is valid 2020-06-16T00:25:29 prefetch.2.10.7: 1) 'SRR1301072' was downloaded successfully Read 8252117 spots for SRR1301072/SRR1301072.sra Written 8252117 spots for SRR1301072/SRR1301072.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: 00:02:41 8252117 reads; of these: 8252117 (100.00%) were unpaired; of these: 267369 (3.24%) aligned 0 times 5880713 (71.26%) aligned exactly 1 time 2104035 (25.50%) aligned >1 times 96.76% overall alignment rate Time searching: 00:02:41 Overall time: 00:02:41 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] 1871614 / 7984748 = 0.2344 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 09:31:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX554724/SRX554724.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX554724/SRX554724.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX554724/SRX554724.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX554724/SRX554724.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 09:31:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:31:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:31:22: 1000000 INFO @ Tue, 16 Jun 2020 09:31:29: 2000000 INFO @ Tue, 16 Jun 2020 09:31:35: 3000000 INFO @ Tue, 16 Jun 2020 09:31:42: 4000000 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 09:31:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX554724/SRX554724.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX554724/SRX554724.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX554724/SRX554724.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX554724/SRX554724.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 09:31:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:31:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:31:49: 5000000 INFO @ Tue, 16 Jun 2020 09:31:53: 1000000 INFO @ Tue, 16 Jun 2020 09:31:56: 6000000 INFO @ Tue, 16 Jun 2020 09:31:57: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:31:57: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:31:57: #1 total tags in treatment: 6113134 INFO @ Tue, 16 Jun 2020 09:31:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:31:57: #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 09:31:57: #1 tags after filtering in treatment: 6113134 INFO @ Tue, 16 Jun 2020 09:31:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:31:57: #1 finished! INFO @ Tue, 16 Jun 2020 09:31:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:31:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:31:58: #2 number of paired peaks: 1520 INFO @ Tue, 16 Jun 2020 09:31:58: start model_add_line... INFO @ Tue, 16 Jun 2020 09:31:58: start X-correlation... INFO @ Tue, 16 Jun 2020 09:31:58: end of X-cor INFO @ Tue, 16 Jun 2020 09:31:58: #2 finished! INFO @ Tue, 16 Jun 2020 09:31:58: #2 predicted fragment length is 68 bps INFO @ Tue, 16 Jun 2020 09:31:58: #2 alternative fragment length(s) may be 2,68,93,592 bps INFO @ Tue, 16 Jun 2020 09:31:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX554724/SRX554724.05_model.r WARNING @ Tue, 16 Jun 2020 09:31:58: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:31:58: #2 You may need to consider one of the other alternative d(s): 2,68,93,592 WARNING @ Tue, 16 Jun 2020 09:31:58: #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 09:31:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:31:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:32:01: 2000000 INFO @ Tue, 16 Jun 2020 09:32:08: 3000000 INFO @ Tue, 16 Jun 2020 09:32:12: #3 Call peaks for each chromosome... 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 09:32:14: 4000000 INFO @ Tue, 16 Jun 2020 09:32:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX554724/SRX554724.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX554724/SRX554724.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX554724/SRX554724.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX554724/SRX554724.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 09:32:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:32:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:32:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX554724/SRX554724.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:32:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX554724/SRX554724.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:32:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX554724/SRX554724.05_summits.bed INFO @ Tue, 16 Jun 2020 09:32:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1122 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:32:22: 5000000 INFO @ Tue, 16 Jun 2020 09:32:23: 1000000 INFO @ Tue, 16 Jun 2020 09:32:30: 6000000 INFO @ Tue, 16 Jun 2020 09:32:30: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:32:30: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:32:30: #1 total tags in treatment: 6113134 INFO @ Tue, 16 Jun 2020 09:32:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:32:30: #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 09:32:30: 2000000 INFO @ Tue, 16 Jun 2020 09:32:30: #1 tags after filtering in treatment: 6113134 INFO @ Tue, 16 Jun 2020 09:32:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:32:30: #1 finished! INFO @ Tue, 16 Jun 2020 09:32:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:32:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:32:31: #2 number of paired peaks: 1520 INFO @ Tue, 16 Jun 2020 09:32:31: start model_add_line... INFO @ Tue, 16 Jun 2020 09:32:31: start X-correlation... INFO @ Tue, 16 Jun 2020 09:32:31: end of X-cor INFO @ Tue, 16 Jun 2020 09:32:31: #2 finished! INFO @ Tue, 16 Jun 2020 09:32:31: #2 predicted fragment length is 68 bps INFO @ Tue, 16 Jun 2020 09:32:31: #2 alternative fragment length(s) may be 2,68,93,592 bps INFO @ Tue, 16 Jun 2020 09:32:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX554724/SRX554724.10_model.r WARNING @ Tue, 16 Jun 2020 09:32:31: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:32:31: #2 You may need to consider one of the other alternative d(s): 2,68,93,592 WARNING @ Tue, 16 Jun 2020 09:32:31: #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 09:32:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:32:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:32:37: 3000000 INFO @ Tue, 16 Jun 2020 09:32:44: 4000000 INFO @ Tue, 16 Jun 2020 09:32:46: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:32:50: 5000000 INFO @ Tue, 16 Jun 2020 09:32:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX554724/SRX554724.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:32:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX554724/SRX554724.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:32:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX554724/SRX554724.10_summits.bed INFO @ Tue, 16 Jun 2020 09:32:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (479 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:32:57: 6000000 INFO @ Tue, 16 Jun 2020 09:32:58: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:32:58: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:32:58: #1 total tags in treatment: 6113134 INFO @ Tue, 16 Jun 2020 09:32:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:32:58: #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 09:32:58: #1 tags after filtering in treatment: 6113134 INFO @ Tue, 16 Jun 2020 09:32:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:32:58: #1 finished! INFO @ Tue, 16 Jun 2020 09:32:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:32:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:32:59: #2 number of paired peaks: 1520 INFO @ Tue, 16 Jun 2020 09:32:59: start model_add_line... INFO @ Tue, 16 Jun 2020 09:32:59: start X-correlation... INFO @ Tue, 16 Jun 2020 09:32:59: end of X-cor INFO @ Tue, 16 Jun 2020 09:32:59: #2 finished! INFO @ Tue, 16 Jun 2020 09:32:59: #2 predicted fragment length is 68 bps INFO @ Tue, 16 Jun 2020 09:32:59: #2 alternative fragment length(s) may be 2,68,93,592 bps INFO @ Tue, 16 Jun 2020 09:32:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX554724/SRX554724.20_model.r WARNING @ Tue, 16 Jun 2020 09:32:59: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:32:59: #2 You may need to consider one of the other alternative d(s): 2,68,93,592 WARNING @ Tue, 16 Jun 2020 09:32:59: #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 09:32:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:32:59: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:33:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:33:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX554724/SRX554724.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:33:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX554724/SRX554724.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:33:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX554724/SRX554724.20_summits.bed INFO @ Tue, 16 Jun 2020 09:33:21: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (160 records, 4 fields): 1 millis CompletedMACS2peakCalling