Job ID = 6367167 SRX = SRX2965741 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:14:46 prefetch.2.10.7: 1) Downloading 'SRR5766326'... 2020-06-15T23:14:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:18:20 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:18:20 prefetch.2.10.7: 1) 'SRR5766326' was downloaded successfully Read 24188927 spots for SRR5766326/SRR5766326.sra Written 24188927 spots for SRR5766326/SRR5766326.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: 00:10:24 24188927 reads; of these: 24188927 (100.00%) were unpaired; of these: 1135502 (4.69%) aligned 0 times 19858417 (82.10%) aligned exactly 1 time 3195008 (13.21%) aligned >1 times 95.31% overall alignment rate Time searching: 00:10:24 Overall time: 00:10:24 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 12 files... [bam_rmdupse_core] 4341521 / 23053425 = 0.1883 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 08:37:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2965741/SRX2965741.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2965741/SRX2965741.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2965741/SRX2965741.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2965741/SRX2965741.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 08:37:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:37:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:37:33: 1000000 INFO @ Tue, 16 Jun 2020 08:37:39: 2000000 INFO @ Tue, 16 Jun 2020 08:37:46: 3000000 INFO @ Tue, 16 Jun 2020 08:37:52: 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 08:37:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2965741/SRX2965741.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2965741/SRX2965741.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2965741/SRX2965741.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2965741/SRX2965741.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 08:37:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:37:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:37:58: 5000000 INFO @ Tue, 16 Jun 2020 08:38:05: 1000000 INFO @ Tue, 16 Jun 2020 08:38:05: 6000000 INFO @ Tue, 16 Jun 2020 08:38:12: 7000000 INFO @ Tue, 16 Jun 2020 08:38:13: 2000000 INFO @ Tue, 16 Jun 2020 08:38:19: 8000000 INFO @ Tue, 16 Jun 2020 08:38:21: 3000000 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 08:38:26: 9000000 INFO @ Tue, 16 Jun 2020 08:38:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2965741/SRX2965741.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2965741/SRX2965741.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2965741/SRX2965741.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2965741/SRX2965741.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 08:38:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:38:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:38:29: 4000000 INFO @ Tue, 16 Jun 2020 08:38:33: 10000000 INFO @ Tue, 16 Jun 2020 08:38:34: 1000000 INFO @ Tue, 16 Jun 2020 08:38:37: 5000000 INFO @ Tue, 16 Jun 2020 08:38:40: 11000000 INFO @ Tue, 16 Jun 2020 08:38:41: 2000000 INFO @ Tue, 16 Jun 2020 08:38:46: 6000000 INFO @ Tue, 16 Jun 2020 08:38:46: 12000000 INFO @ Tue, 16 Jun 2020 08:38:48: 3000000 INFO @ Tue, 16 Jun 2020 08:38:53: 13000000 INFO @ Tue, 16 Jun 2020 08:38:54: 7000000 INFO @ Tue, 16 Jun 2020 08:38:54: 4000000 INFO @ Tue, 16 Jun 2020 08:39:00: 14000000 INFO @ Tue, 16 Jun 2020 08:39:01: 5000000 INFO @ Tue, 16 Jun 2020 08:39:02: 8000000 INFO @ Tue, 16 Jun 2020 08:39:07: 15000000 INFO @ Tue, 16 Jun 2020 08:39:08: 6000000 INFO @ Tue, 16 Jun 2020 08:39:10: 9000000 INFO @ Tue, 16 Jun 2020 08:39:14: 16000000 INFO @ Tue, 16 Jun 2020 08:39:15: 7000000 INFO @ Tue, 16 Jun 2020 08:39:18: 10000000 INFO @ Tue, 16 Jun 2020 08:39:21: 17000000 INFO @ Tue, 16 Jun 2020 08:39:22: 8000000 INFO @ Tue, 16 Jun 2020 08:39:26: 11000000 INFO @ Tue, 16 Jun 2020 08:39:27: 18000000 INFO @ Tue, 16 Jun 2020 08:39:29: 9000000 INFO @ Tue, 16 Jun 2020 08:39:32: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:39:32: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:39:32: #1 total tags in treatment: 18711904 INFO @ Tue, 16 Jun 2020 08:39:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:39:32: #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 08:39:33: #1 tags after filtering in treatment: 18711904 INFO @ Tue, 16 Jun 2020 08:39:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:39:33: #1 finished! INFO @ Tue, 16 Jun 2020 08:39:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:39:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:39:33: 12000000 INFO @ Tue, 16 Jun 2020 08:39:34: #2 number of paired peaks: 1756 INFO @ Tue, 16 Jun 2020 08:39:34: start model_add_line... INFO @ Tue, 16 Jun 2020 08:39:34: start X-correlation... INFO @ Tue, 16 Jun 2020 08:39:34: end of X-cor INFO @ Tue, 16 Jun 2020 08:39:34: #2 finished! INFO @ Tue, 16 Jun 2020 08:39:34: #2 predicted fragment length is 166 bps INFO @ Tue, 16 Jun 2020 08:39:34: #2 alternative fragment length(s) may be 166 bps INFO @ Tue, 16 Jun 2020 08:39:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2965741/SRX2965741.05_model.r WARNING @ Tue, 16 Jun 2020 08:39:34: #2 Since the d (166) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:39:34: #2 You may need to consider one of the other alternative d(s): 166 WARNING @ Tue, 16 Jun 2020 08:39:34: #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 08:39:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:39:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:39:36: 10000000 INFO @ Tue, 16 Jun 2020 08:39:41: 13000000 INFO @ Tue, 16 Jun 2020 08:39:42: 11000000 INFO @ Tue, 16 Jun 2020 08:39:48: 14000000 INFO @ Tue, 16 Jun 2020 08:39:49: 12000000 INFO @ Tue, 16 Jun 2020 08:39:56: 13000000 INFO @ Tue, 16 Jun 2020 08:39:56: 15000000 INFO @ Tue, 16 Jun 2020 08:40:02: 14000000 INFO @ Tue, 16 Jun 2020 08:40:03: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:40:09: 15000000 INFO @ Tue, 16 Jun 2020 08:40:11: 17000000 INFO @ Tue, 16 Jun 2020 08:40:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:40:15: 16000000 INFO @ Tue, 16 Jun 2020 08:40:18: 18000000 INFO @ Tue, 16 Jun 2020 08:40:22: 17000000 INFO @ Tue, 16 Jun 2020 08:40:23: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:40:23: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:40:23: #1 total tags in treatment: 18711904 INFO @ Tue, 16 Jun 2020 08:40:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:40:23: #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 08:40:24: #1 tags after filtering in treatment: 18711904 INFO @ Tue, 16 Jun 2020 08:40:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:40:24: #1 finished! INFO @ Tue, 16 Jun 2020 08:40:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:40:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:40:25: #2 number of paired peaks: 1756 INFO @ Tue, 16 Jun 2020 08:40:25: start model_add_line... INFO @ Tue, 16 Jun 2020 08:40:25: start X-correlation... INFO @ Tue, 16 Jun 2020 08:40:25: end of X-cor INFO @ Tue, 16 Jun 2020 08:40:25: #2 finished! INFO @ Tue, 16 Jun 2020 08:40:25: #2 predicted fragment length is 166 bps INFO @ Tue, 16 Jun 2020 08:40:25: #2 alternative fragment length(s) may be 166 bps INFO @ Tue, 16 Jun 2020 08:40:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2965741/SRX2965741.10_model.r WARNING @ Tue, 16 Jun 2020 08:40:25: #2 Since the d (166) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:40:25: #2 You may need to consider one of the other alternative d(s): 166 WARNING @ Tue, 16 Jun 2020 08:40:25: #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 08:40:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:40:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:40:28: 18000000 INFO @ Tue, 16 Jun 2020 08:40:32: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:40:32: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:40:32: #1 total tags in treatment: 18711904 INFO @ Tue, 16 Jun 2020 08:40:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:40:32: #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 08:40:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2965741/SRX2965741.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:40:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2965741/SRX2965741.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:40:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2965741/SRX2965741.05_summits.bed INFO @ Tue, 16 Jun 2020 08:40:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5481 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:40:33: #1 tags after filtering in treatment: 18711904 INFO @ Tue, 16 Jun 2020 08:40:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:40:33: #1 finished! INFO @ Tue, 16 Jun 2020 08:40:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:40:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:40:34: #2 number of paired peaks: 1756 INFO @ Tue, 16 Jun 2020 08:40:34: start model_add_line... INFO @ Tue, 16 Jun 2020 08:40:34: start X-correlation... INFO @ Tue, 16 Jun 2020 08:40:34: end of X-cor INFO @ Tue, 16 Jun 2020 08:40:34: #2 finished! INFO @ Tue, 16 Jun 2020 08:40:34: #2 predicted fragment length is 166 bps INFO @ Tue, 16 Jun 2020 08:40:34: #2 alternative fragment length(s) may be 166 bps INFO @ Tue, 16 Jun 2020 08:40:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2965741/SRX2965741.20_model.r WARNING @ Tue, 16 Jun 2020 08:40:34: #2 Since the d (166) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:40:34: #2 You may need to consider one of the other alternative d(s): 166 WARNING @ Tue, 16 Jun 2020 08:40:34: #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 08:40:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:40:34: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:41:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:41:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:41:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2965741/SRX2965741.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:41:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2965741/SRX2965741.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:41:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2965741/SRX2965741.10_summits.bed INFO @ Tue, 16 Jun 2020 08:41:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4242 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:41:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2965741/SRX2965741.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:41:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2965741/SRX2965741.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:41:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2965741/SRX2965741.20_summits.bed INFO @ Tue, 16 Jun 2020 08:41:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3139 records, 4 fields): 5 millis CompletedMACS2peakCalling