Job ID = 6367359 SRX = SRX331118 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:31:35 prefetch.2.10.7: 1) Downloading 'SRR947349'... 2020-06-15T23:31:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:32:37 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:32:37 prefetch.2.10.7: 'SRR947349' is valid 2020-06-15T23:32:37 prefetch.2.10.7: 1) 'SRR947349' was downloaded successfully Read 8476444 spots for SRR947349/SRR947349.sra Written 8476444 spots for SRR947349/SRR947349.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: 00:01:00 8476444 reads; of these: 8476444 (100.00%) were unpaired; of these: 3705171 (43.71%) aligned 0 times 3998110 (47.17%) aligned exactly 1 time 773163 (9.12%) aligned >1 times 56.29% overall alignment rate Time searching: 00:01:00 Overall time: 00:01:00 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] 643220 / 4771273 = 0.1348 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 08:35:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331118/SRX331118.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331118/SRX331118.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331118/SRX331118.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331118/SRX331118.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 08:35:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:35:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:35:38: 1000000 INFO @ Tue, 16 Jun 2020 08:35:44: 2000000 INFO @ Tue, 16 Jun 2020 08:35:49: 3000000 INFO @ Tue, 16 Jun 2020 08:35:55: 4000000 INFO @ Tue, 16 Jun 2020 08:35:56: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:35:56: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:35:56: #1 total tags in treatment: 4128053 INFO @ Tue, 16 Jun 2020 08:35:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:35:56: #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 08:35:56: #1 tags after filtering in treatment: 4128053 INFO @ Tue, 16 Jun 2020 08:35:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:35:56: #1 finished! INFO @ Tue, 16 Jun 2020 08:35:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:35:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:35:56: #2 number of paired peaks: 457 WARNING @ Tue, 16 Jun 2020 08:35:56: Fewer paired peaks (457) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 457 pairs to build model! INFO @ Tue, 16 Jun 2020 08:35:56: start model_add_line... INFO @ Tue, 16 Jun 2020 08:35:56: start X-correlation... INFO @ Tue, 16 Jun 2020 08:35:56: end of X-cor INFO @ Tue, 16 Jun 2020 08:35:56: #2 finished! INFO @ Tue, 16 Jun 2020 08:35:56: #2 predicted fragment length is 96 bps INFO @ Tue, 16 Jun 2020 08:35:56: #2 alternative fragment length(s) may be 79,96 bps INFO @ Tue, 16 Jun 2020 08:35:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331118/SRX331118.05_model.r INFO @ Tue, 16 Jun 2020 08:35:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:35:56: #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 08:36:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331118/SRX331118.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331118/SRX331118.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331118/SRX331118.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331118/SRX331118.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 08:36:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:36:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:36:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:36:09: 1000000 INFO @ Tue, 16 Jun 2020 08:36:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331118/SRX331118.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:36:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331118/SRX331118.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:36:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331118/SRX331118.05_summits.bed INFO @ Tue, 16 Jun 2020 08:36:10: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1179 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:36:16: 2000000 INFO @ Tue, 16 Jun 2020 08:36:22: 3000000 INFO @ Tue, 16 Jun 2020 08:36:29: 4000000 INFO @ Tue, 16 Jun 2020 08:36:30: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:36:30: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:36:30: #1 total tags in treatment: 4128053 INFO @ Tue, 16 Jun 2020 08:36:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:36:30: #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 08:36:30: #1 tags after filtering in treatment: 4128053 INFO @ Tue, 16 Jun 2020 08:36:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:36:30: #1 finished! INFO @ Tue, 16 Jun 2020 08:36:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:36:30: #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 08:36:30: #2 number of paired peaks: 457 WARNING @ Tue, 16 Jun 2020 08:36:30: Fewer paired peaks (457) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 457 pairs to build model! INFO @ Tue, 16 Jun 2020 08:36:30: start model_add_line... INFO @ Tue, 16 Jun 2020 08:36:30: start X-correlation... INFO @ Tue, 16 Jun 2020 08:36:30: end of X-cor INFO @ Tue, 16 Jun 2020 08:36:30: #2 finished! INFO @ Tue, 16 Jun 2020 08:36:30: #2 predicted fragment length is 96 bps INFO @ Tue, 16 Jun 2020 08:36:30: #2 alternative fragment length(s) may be 79,96 bps INFO @ Tue, 16 Jun 2020 08:36:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331118/SRX331118.10_model.r INFO @ Tue, 16 Jun 2020 08:36:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:36:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:36:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331118/SRX331118.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331118/SRX331118.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331118/SRX331118.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331118/SRX331118.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 08:36:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:36:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:36:38: 1000000 INFO @ Tue, 16 Jun 2020 08:36:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:36:43: 2000000 INFO @ Tue, 16 Jun 2020 08:36:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331118/SRX331118.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:36:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331118/SRX331118.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:36:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331118/SRX331118.10_summits.bed INFO @ Tue, 16 Jun 2020 08:36:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (532 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:36:49: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:36:55: 4000000 INFO @ Tue, 16 Jun 2020 08:36:55: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:36:55: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:36:55: #1 total tags in treatment: 4128053 INFO @ Tue, 16 Jun 2020 08:36:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:36:55: #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 08:36:55: #1 tags after filtering in treatment: 4128053 INFO @ Tue, 16 Jun 2020 08:36:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:36:55: #1 finished! INFO @ Tue, 16 Jun 2020 08:36:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:36:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:36:56: #2 number of paired peaks: 457 WARNING @ Tue, 16 Jun 2020 08:36:56: Fewer paired peaks (457) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 457 pairs to build model! INFO @ Tue, 16 Jun 2020 08:36:56: start model_add_line... INFO @ Tue, 16 Jun 2020 08:36:56: start X-correlation... INFO @ Tue, 16 Jun 2020 08:36:56: end of X-cor INFO @ Tue, 16 Jun 2020 08:36:56: #2 finished! INFO @ Tue, 16 Jun 2020 08:36:56: #2 predicted fragment length is 96 bps INFO @ Tue, 16 Jun 2020 08:36:56: #2 alternative fragment length(s) may be 79,96 bps INFO @ Tue, 16 Jun 2020 08:36:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331118/SRX331118.20_model.r INFO @ Tue, 16 Jun 2020 08:36:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:36:56: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:37:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:37:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331118/SRX331118.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:37:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331118/SRX331118.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:37:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331118/SRX331118.20_summits.bed INFO @ Tue, 16 Jun 2020 08:37:10: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (167 records, 4 fields): 1 millis CompletedMACS2peakCalling