Job ID = 6367487 SRX = SRX331244 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:02:30 prefetch.2.10.7: 1) Downloading 'SRR947476'... 2020-06-16T00:02:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:02:55 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:02:55 prefetch.2.10.7: 'SRR947476' is valid 2020-06-16T00:02:55 prefetch.2.10.7: 1) 'SRR947476' was downloaded successfully Read 7439152 spots for SRR947476/SRR947476.sra Written 7439152 spots for SRR947476/SRR947476.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: 00:01:11 7439152 reads; of these: 7439152 (100.00%) were unpaired; of these: 317350 (4.27%) aligned 0 times 5972307 (80.28%) aligned exactly 1 time 1149495 (15.45%) aligned >1 times 95.73% overall alignment rate Time searching: 00:01:11 Overall time: 00:01:11 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] 899986 / 7121802 = 0.1264 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 09:06:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331244/SRX331244.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331244/SRX331244.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331244/SRX331244.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331244/SRX331244.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 09:06:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:06:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:06:39: 1000000 INFO @ Tue, 16 Jun 2020 09:06:44: 2000000 INFO @ Tue, 16 Jun 2020 09:06:48: 3000000 INFO @ Tue, 16 Jun 2020 09:06:53: 4000000 INFO @ Tue, 16 Jun 2020 09:06:57: 5000000 INFO @ Tue, 16 Jun 2020 09:07:01: 6000000 INFO @ Tue, 16 Jun 2020 09:07:02: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 09:07:02: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 09:07:02: #1 total tags in treatment: 6221816 INFO @ Tue, 16 Jun 2020 09:07:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:07:02: #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 09:07:02: #1 tags after filtering in treatment: 6221816 INFO @ Tue, 16 Jun 2020 09:07:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:07:02: #1 finished! INFO @ Tue, 16 Jun 2020 09:07:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:07:02: #2 looking for paired plus/minus strand peaks... 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 09:07:03: #2 number of paired peaks: 460 WARNING @ Tue, 16 Jun 2020 09:07:03: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Tue, 16 Jun 2020 09:07:03: start model_add_line... INFO @ Tue, 16 Jun 2020 09:07:03: start X-correlation... INFO @ Tue, 16 Jun 2020 09:07:03: end of X-cor INFO @ Tue, 16 Jun 2020 09:07:03: #2 finished! INFO @ Tue, 16 Jun 2020 09:07:03: #2 predicted fragment length is 76 bps INFO @ Tue, 16 Jun 2020 09:07:03: #2 alternative fragment length(s) may be 4,40,76,88,116,120,590 bps INFO @ Tue, 16 Jun 2020 09:07:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331244/SRX331244.05_model.r INFO @ Tue, 16 Jun 2020 09:07:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:07:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:07:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331244/SRX331244.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331244/SRX331244.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331244/SRX331244.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331244/SRX331244.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 09:07:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:07:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:07:09: 1000000 INFO @ Tue, 16 Jun 2020 09:07:14: 2000000 INFO @ Tue, 16 Jun 2020 09:07:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:07:18: 3000000 INFO @ Tue, 16 Jun 2020 09:07:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331244/SRX331244.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:07:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331244/SRX331244.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:07:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331244/SRX331244.05_summits.bed INFO @ Tue, 16 Jun 2020 09:07:21: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1152 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:07:23: 4000000 INFO @ Tue, 16 Jun 2020 09:07:27: 5000000 INFO @ Tue, 16 Jun 2020 09:07:31: 6000000 INFO @ Tue, 16 Jun 2020 09:07:32: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 09:07:32: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 09:07:32: #1 total tags in treatment: 6221816 INFO @ Tue, 16 Jun 2020 09:07:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:07:32: #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 09:07:33: #1 tags after filtering in treatment: 6221816 INFO @ Tue, 16 Jun 2020 09:07:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:07:33: #1 finished! INFO @ Tue, 16 Jun 2020 09:07:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:07:33: #2 looking for paired plus/minus strand peaks... 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 09:07:33: #2 number of paired peaks: 460 WARNING @ Tue, 16 Jun 2020 09:07:33: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Tue, 16 Jun 2020 09:07:33: start model_add_line... INFO @ Tue, 16 Jun 2020 09:07:33: start X-correlation... INFO @ Tue, 16 Jun 2020 09:07:33: end of X-cor INFO @ Tue, 16 Jun 2020 09:07:33: #2 finished! INFO @ Tue, 16 Jun 2020 09:07:33: #2 predicted fragment length is 76 bps INFO @ Tue, 16 Jun 2020 09:07:33: #2 alternative fragment length(s) may be 4,40,76,88,116,120,590 bps INFO @ Tue, 16 Jun 2020 09:07:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331244/SRX331244.10_model.r INFO @ Tue, 16 Jun 2020 09:07:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:07:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:07:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331244/SRX331244.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331244/SRX331244.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331244/SRX331244.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331244/SRX331244.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 09:07:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:07:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:07:40: 1000000 INFO @ Tue, 16 Jun 2020 09:07:44: 2000000 INFO @ Tue, 16 Jun 2020 09:07:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:07:48: 3000000 INFO @ Tue, 16 Jun 2020 09:07:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331244/SRX331244.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:07:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331244/SRX331244.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:07:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331244/SRX331244.10_summits.bed INFO @ Tue, 16 Jun 2020 09:07:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (553 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:07:53: 4000000 INFO @ Tue, 16 Jun 2020 09:07:57: 5000000 INFO @ Tue, 16 Jun 2020 09:08:02: 6000000 INFO @ Tue, 16 Jun 2020 09:08:03: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 09:08:03: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 09:08:03: #1 total tags in treatment: 6221816 INFO @ Tue, 16 Jun 2020 09:08:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:08:03: #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 09:08:03: #1 tags after filtering in treatment: 6221816 INFO @ Tue, 16 Jun 2020 09:08:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:08:03: #1 finished! INFO @ Tue, 16 Jun 2020 09:08:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:08:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:08:03: #2 number of paired peaks: 460 WARNING @ Tue, 16 Jun 2020 09:08:03: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Tue, 16 Jun 2020 09:08:03: start model_add_line... INFO @ Tue, 16 Jun 2020 09:08:03: start X-correlation... INFO @ Tue, 16 Jun 2020 09:08:03: end of X-cor INFO @ Tue, 16 Jun 2020 09:08:03: #2 finished! INFO @ Tue, 16 Jun 2020 09:08:03: #2 predicted fragment length is 76 bps INFO @ Tue, 16 Jun 2020 09:08:03: #2 alternative fragment length(s) may be 4,40,76,88,116,120,590 bps INFO @ Tue, 16 Jun 2020 09:08:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331244/SRX331244.20_model.r INFO @ Tue, 16 Jun 2020 09:08:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:08:03: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:08:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:08:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331244/SRX331244.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:08:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331244/SRX331244.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:08:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331244/SRX331244.20_summits.bed INFO @ Tue, 16 Jun 2020 09:08:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (216 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。