Job ID = 6366917 SRX = SRX2576620 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:06:38 prefetch.2.10.7: 1) Downloading 'SRR5272577'... 2020-06-15T23:06:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:07:52 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:07:53 prefetch.2.10.7: 'SRR5272577' is valid 2020-06-15T23:07:53 prefetch.2.10.7: 1) 'SRR5272577' was downloaded successfully Read 15742148 spots for SRR5272577/SRR5272577.sra Written 15742148 spots for SRR5272577/SRR5272577.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: 00:02:31 15742148 reads; of these: 15742148 (100.00%) were unpaired; of these: 802553 (5.10%) aligned 0 times 12310210 (78.20%) aligned exactly 1 time 2629385 (16.70%) aligned >1 times 94.90% overall alignment rate Time searching: 00:02:31 Overall time: 00:02:31 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] 2246791 / 14939595 = 0.1504 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 08:14:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576620/SRX2576620.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576620/SRX2576620.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576620/SRX2576620.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576620/SRX2576620.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 08:14:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:14:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:14:44: 1000000 INFO @ Tue, 16 Jun 2020 08:14:48: 2000000 INFO @ Tue, 16 Jun 2020 08:14:53: 3000000 INFO @ Tue, 16 Jun 2020 08:14:58: 4000000 INFO @ Tue, 16 Jun 2020 08:15:03: 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 08:15:08: 6000000 INFO @ Tue, 16 Jun 2020 08:15:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576620/SRX2576620.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576620/SRX2576620.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576620/SRX2576620.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576620/SRX2576620.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 08:15:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:15:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:15:13: 7000000 INFO @ Tue, 16 Jun 2020 08:15:15: 1000000 INFO @ Tue, 16 Jun 2020 08:15:18: 8000000 INFO @ Tue, 16 Jun 2020 08:15:21: 2000000 INFO @ Tue, 16 Jun 2020 08:15:23: 9000000 INFO @ Tue, 16 Jun 2020 08:15:27: 3000000 INFO @ Tue, 16 Jun 2020 08:15:28: 10000000 INFO @ Tue, 16 Jun 2020 08:15:33: 11000000 INFO @ Tue, 16 Jun 2020 08:15:33: 4000000 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 08:15:38: 12000000 INFO @ Tue, 16 Jun 2020 08:15:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576620/SRX2576620.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576620/SRX2576620.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576620/SRX2576620.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576620/SRX2576620.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 08:15:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:15:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:15:39: 5000000 INFO @ Tue, 16 Jun 2020 08:15:42: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:15:42: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:15:42: #1 total tags in treatment: 12692804 INFO @ Tue, 16 Jun 2020 08:15:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:15:42: #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 08:15:42: #1 tags after filtering in treatment: 12692804 INFO @ Tue, 16 Jun 2020 08:15:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:15:42: #1 finished! INFO @ Tue, 16 Jun 2020 08:15:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:15:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:15:43: #2 number of paired peaks: 494 WARNING @ Tue, 16 Jun 2020 08:15:43: Fewer paired peaks (494) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 494 pairs to build model! INFO @ Tue, 16 Jun 2020 08:15:43: start model_add_line... INFO @ Tue, 16 Jun 2020 08:15:43: start X-correlation... INFO @ Tue, 16 Jun 2020 08:15:43: end of X-cor INFO @ Tue, 16 Jun 2020 08:15:43: #2 finished! INFO @ Tue, 16 Jun 2020 08:15:43: #2 predicted fragment length is 132 bps INFO @ Tue, 16 Jun 2020 08:15:43: #2 alternative fragment length(s) may be 132 bps INFO @ Tue, 16 Jun 2020 08:15:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576620/SRX2576620.05_model.r INFO @ Tue, 16 Jun 2020 08:15:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:15:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:15:44: 1000000 INFO @ Tue, 16 Jun 2020 08:15:46: 6000000 INFO @ Tue, 16 Jun 2020 08:15:50: 2000000 INFO @ Tue, 16 Jun 2020 08:15:52: 7000000 INFO @ Tue, 16 Jun 2020 08:15:56: 3000000 INFO @ Tue, 16 Jun 2020 08:15:58: 8000000 INFO @ Tue, 16 Jun 2020 08:16:01: 4000000 INFO @ Tue, 16 Jun 2020 08:16:04: 9000000 INFO @ Tue, 16 Jun 2020 08:16:07: 5000000 INFO @ Tue, 16 Jun 2020 08:16:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:16:10: 10000000 INFO @ Tue, 16 Jun 2020 08:16:13: 6000000 INFO @ Tue, 16 Jun 2020 08:16:17: 11000000 INFO @ Tue, 16 Jun 2020 08:16:19: 7000000 INFO @ Tue, 16 Jun 2020 08:16:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576620/SRX2576620.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:16:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576620/SRX2576620.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:16:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576620/SRX2576620.05_summits.bed INFO @ Tue, 16 Jun 2020 08:16:22: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2437 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:16:23: 12000000 INFO @ Tue, 16 Jun 2020 08:16:24: 8000000 INFO @ Tue, 16 Jun 2020 08:16:27: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:16:27: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:16:27: #1 total tags in treatment: 12692804 INFO @ Tue, 16 Jun 2020 08:16:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:16:27: #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 08:16:28: #1 tags after filtering in treatment: 12692804 INFO @ Tue, 16 Jun 2020 08:16:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:16:28: #1 finished! INFO @ Tue, 16 Jun 2020 08:16:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:16:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:16:29: #2 number of paired peaks: 494 WARNING @ Tue, 16 Jun 2020 08:16:29: Fewer paired peaks (494) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 494 pairs to build model! INFO @ Tue, 16 Jun 2020 08:16:29: start model_add_line... INFO @ Tue, 16 Jun 2020 08:16:29: start X-correlation... INFO @ Tue, 16 Jun 2020 08:16:29: end of X-cor INFO @ Tue, 16 Jun 2020 08:16:29: #2 finished! INFO @ Tue, 16 Jun 2020 08:16:29: #2 predicted fragment length is 132 bps INFO @ Tue, 16 Jun 2020 08:16:29: #2 alternative fragment length(s) may be 132 bps INFO @ Tue, 16 Jun 2020 08:16:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576620/SRX2576620.10_model.r INFO @ Tue, 16 Jun 2020 08:16:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:16:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:16:30: 9000000 INFO @ Tue, 16 Jun 2020 08:16:36: 10000000 INFO @ Tue, 16 Jun 2020 08:16:41: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:16:47: 12000000 INFO @ Tue, 16 Jun 2020 08:16:51: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:16:51: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:16:51: #1 total tags in treatment: 12692804 INFO @ Tue, 16 Jun 2020 08:16:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:16:51: #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 08:16:52: #1 tags after filtering in treatment: 12692804 INFO @ Tue, 16 Jun 2020 08:16:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:16:52: #1 finished! INFO @ Tue, 16 Jun 2020 08:16:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:16:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:16:53: #2 number of paired peaks: 494 WARNING @ Tue, 16 Jun 2020 08:16:53: Fewer paired peaks (494) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 494 pairs to build model! INFO @ Tue, 16 Jun 2020 08:16:53: start model_add_line... INFO @ Tue, 16 Jun 2020 08:16:53: start X-correlation... INFO @ Tue, 16 Jun 2020 08:16:53: end of X-cor INFO @ Tue, 16 Jun 2020 08:16:53: #2 finished! INFO @ Tue, 16 Jun 2020 08:16:53: #2 predicted fragment length is 132 bps INFO @ Tue, 16 Jun 2020 08:16:53: #2 alternative fragment length(s) may be 132 bps INFO @ Tue, 16 Jun 2020 08:16:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576620/SRX2576620.20_model.r INFO @ Tue, 16 Jun 2020 08:16:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:16:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:16:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:17:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576620/SRX2576620.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:17:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576620/SRX2576620.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:17:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576620/SRX2576620.10_summits.bed INFO @ Tue, 16 Jun 2020 08:17:09: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1730 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:17:20: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:17:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576620/SRX2576620.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:17:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576620/SRX2576620.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:17:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576620/SRX2576620.20_summits.bed INFO @ Tue, 16 Jun 2020 08:17:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1151 records, 4 fields): 3 millis CompletedMACS2peakCalling