Job ID = 6367069 SRX = SRX277026 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:05:23 prefetch.2.10.7: 1) Downloading 'SRR849695'... 2020-06-15T23:05:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:05:43 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:05:43 prefetch.2.10.7: 'SRR849695' is valid 2020-06-15T23:05:43 prefetch.2.10.7: 1) 'SRR849695' was downloaded successfully Read 2648379 spots for SRR849695/SRR849695.sra Written 2648379 spots for SRR849695/SRR849695.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: 00:00:17 2648379 reads; of these: 2648379 (100.00%) were unpaired; of these: 875145 (33.04%) aligned 0 times 1511819 (57.08%) aligned exactly 1 time 261415 (9.87%) aligned >1 times 66.96% overall alignment rate Time searching: 00:00:17 Overall time: 00:00:17 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] 82622 / 1773234 = 0.0466 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 08:06:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277026/SRX277026.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277026/SRX277026.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277026/SRX277026.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277026/SRX277026.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 08:06:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:06:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:07:02: 1000000 INFO @ Tue, 16 Jun 2020 08:07:05: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:07:05: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:07:05: #1 total tags in treatment: 1690612 INFO @ Tue, 16 Jun 2020 08:07:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:07:05: #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 08:07:05: #1 tags after filtering in treatment: 1690612 INFO @ Tue, 16 Jun 2020 08:07:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:07:05: #1 finished! INFO @ Tue, 16 Jun 2020 08:07:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:07:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:07:06: #2 number of paired peaks: 948 WARNING @ Tue, 16 Jun 2020 08:07:06: Fewer paired peaks (948) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 948 pairs to build model! INFO @ Tue, 16 Jun 2020 08:07:06: start model_add_line... INFO @ Tue, 16 Jun 2020 08:07:06: start X-correlation... INFO @ Tue, 16 Jun 2020 08:07:06: end of X-cor INFO @ Tue, 16 Jun 2020 08:07:06: #2 finished! INFO @ Tue, 16 Jun 2020 08:07:06: #2 predicted fragment length is 155 bps INFO @ Tue, 16 Jun 2020 08:07:06: #2 alternative fragment length(s) may be 155 bps INFO @ Tue, 16 Jun 2020 08:07:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277026/SRX277026.05_model.r INFO @ Tue, 16 Jun 2020 08:07:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:07:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:07:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:07:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277026/SRX277026.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:07:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277026/SRX277026.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:07:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277026/SRX277026.05_summits.bed INFO @ Tue, 16 Jun 2020 08:07:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1502 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 08:07:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277026/SRX277026.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277026/SRX277026.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277026/SRX277026.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277026/SRX277026.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 08:07:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:07:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:07:32: 1000000 INFO @ Tue, 16 Jun 2020 08:07:35: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:07:35: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:07:35: #1 total tags in treatment: 1690612 INFO @ Tue, 16 Jun 2020 08:07:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:07:35: #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 08:07:35: #1 tags after filtering in treatment: 1690612 INFO @ Tue, 16 Jun 2020 08:07:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:07:35: #1 finished! INFO @ Tue, 16 Jun 2020 08:07:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:07:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:07:36: #2 number of paired peaks: 948 WARNING @ Tue, 16 Jun 2020 08:07:36: Fewer paired peaks (948) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 948 pairs to build model! INFO @ Tue, 16 Jun 2020 08:07:36: start model_add_line... INFO @ Tue, 16 Jun 2020 08:07:36: start X-correlation... INFO @ Tue, 16 Jun 2020 08:07:36: end of X-cor INFO @ Tue, 16 Jun 2020 08:07:36: #2 finished! INFO @ Tue, 16 Jun 2020 08:07:36: #2 predicted fragment length is 155 bps INFO @ Tue, 16 Jun 2020 08:07:36: #2 alternative fragment length(s) may be 155 bps INFO @ Tue, 16 Jun 2020 08:07:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277026/SRX277026.10_model.r INFO @ Tue, 16 Jun 2020 08:07:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:07:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:07:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:07:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277026/SRX277026.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:07:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277026/SRX277026.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:07:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277026/SRX277026.10_summits.bed INFO @ Tue, 16 Jun 2020 08:07:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (591 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 08:07:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX277026/SRX277026.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX277026/SRX277026.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX277026/SRX277026.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX277026/SRX277026.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 08:07:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:07:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:08:02: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:08:06: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:08:06: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:08:06: #1 total tags in treatment: 1690612 INFO @ Tue, 16 Jun 2020 08:08:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:08:06: #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 08:08:06: #1 tags after filtering in treatment: 1690612 INFO @ Tue, 16 Jun 2020 08:08:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:08:06: #1 finished! INFO @ Tue, 16 Jun 2020 08:08:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:08:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:08:06: #2 number of paired peaks: 948 WARNING @ Tue, 16 Jun 2020 08:08:06: Fewer paired peaks (948) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 948 pairs to build model! INFO @ Tue, 16 Jun 2020 08:08:06: start model_add_line... INFO @ Tue, 16 Jun 2020 08:08:06: start X-correlation... INFO @ Tue, 16 Jun 2020 08:08:06: end of X-cor INFO @ Tue, 16 Jun 2020 08:08:06: #2 finished! INFO @ Tue, 16 Jun 2020 08:08:06: #2 predicted fragment length is 155 bps INFO @ Tue, 16 Jun 2020 08:08:06: #2 alternative fragment length(s) may be 155 bps INFO @ Tue, 16 Jun 2020 08:08:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX277026/SRX277026.20_model.r INFO @ Tue, 16 Jun 2020 08:08:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:08:06: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:08:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:08:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX277026/SRX277026.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:08:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX277026/SRX277026.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:08:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX277026/SRX277026.20_summits.bed INFO @ Tue, 16 Jun 2020 08:08:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (200 records, 4 fields): 1 millis CompletedMACS2peakCalling