Job ID = 6368409 SRX = SRX495088 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:06:01 prefetch.2.10.7: 1) Downloading 'SRR1198620'... 2020-06-16T00:06:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:07:33 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:07:34 prefetch.2.10.7: 'SRR1198620' is valid 2020-06-16T00:07:34 prefetch.2.10.7: 1) 'SRR1198620' was downloaded successfully Read 13944143 spots for SRR1198620/SRR1198620.sra Written 13944143 spots for SRR1198620/SRR1198620.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: 00:02:07 13944143 reads; of these: 13944143 (100.00%) were unpaired; of these: 2407306 (17.26%) aligned 0 times 9745122 (69.89%) aligned exactly 1 time 1791715 (12.85%) aligned >1 times 82.74% overall alignment rate Time searching: 00:02:07 Overall time: 00:02:07 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] 5120019 / 11536837 = 0.4438 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 09:13:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495088/SRX495088.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495088/SRX495088.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495088/SRX495088.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495088/SRX495088.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 09:13:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:13:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:13:23: 1000000 INFO @ Tue, 16 Jun 2020 09:13:28: 2000000 INFO @ Tue, 16 Jun 2020 09:13:33: 3000000 INFO @ Tue, 16 Jun 2020 09:13:37: 4000000 INFO @ Tue, 16 Jun 2020 09:13:42: 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 09:13:46: 6000000 INFO @ Tue, 16 Jun 2020 09:13:48: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:13:48: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:13:48: #1 total tags in treatment: 6416818 INFO @ Tue, 16 Jun 2020 09:13:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:13:48: #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 09:13:48: #1 tags after filtering in treatment: 6416818 INFO @ Tue, 16 Jun 2020 09:13:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:13:48: #1 finished! INFO @ Tue, 16 Jun 2020 09:13:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:13:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:13:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495088/SRX495088.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495088/SRX495088.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495088/SRX495088.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495088/SRX495088.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 09:13:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:13:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:13:49: #2 number of paired peaks: 1384 INFO @ Tue, 16 Jun 2020 09:13:49: start model_add_line... INFO @ Tue, 16 Jun 2020 09:13:49: start X-correlation... INFO @ Tue, 16 Jun 2020 09:13:49: end of X-cor INFO @ Tue, 16 Jun 2020 09:13:49: #2 finished! INFO @ Tue, 16 Jun 2020 09:13:49: #2 predicted fragment length is 215 bps INFO @ Tue, 16 Jun 2020 09:13:49: #2 alternative fragment length(s) may be 215 bps INFO @ Tue, 16 Jun 2020 09:13:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495088/SRX495088.05_model.r INFO @ Tue, 16 Jun 2020 09:13:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:13:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:13:54: 1000000 INFO @ Tue, 16 Jun 2020 09:13:59: 2000000 INFO @ Tue, 16 Jun 2020 09:14:05: 3000000 INFO @ Tue, 16 Jun 2020 09:14:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:14:10: 4000000 INFO @ Tue, 16 Jun 2020 09:14:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495088/SRX495088.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:14:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495088/SRX495088.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:14:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495088/SRX495088.05_summits.bed INFO @ Tue, 16 Jun 2020 09:14:13: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3158 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:14:15: 5000000 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 09:14:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495088/SRX495088.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495088/SRX495088.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495088/SRX495088.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495088/SRX495088.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 09:14:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:14:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:14:20: 6000000 INFO @ Tue, 16 Jun 2020 09:14:22: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:14:22: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:14:22: #1 total tags in treatment: 6416818 INFO @ Tue, 16 Jun 2020 09:14:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:14:22: #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 09:14:22: #1 tags after filtering in treatment: 6416818 INFO @ Tue, 16 Jun 2020 09:14:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:14:22: #1 finished! INFO @ Tue, 16 Jun 2020 09:14:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:14:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:14:23: 1000000 INFO @ Tue, 16 Jun 2020 09:14:23: #2 number of paired peaks: 1384 INFO @ Tue, 16 Jun 2020 09:14:23: start model_add_line... INFO @ Tue, 16 Jun 2020 09:14:23: start X-correlation... INFO @ Tue, 16 Jun 2020 09:14:23: end of X-cor INFO @ Tue, 16 Jun 2020 09:14:23: #2 finished! INFO @ Tue, 16 Jun 2020 09:14:23: #2 predicted fragment length is 215 bps INFO @ Tue, 16 Jun 2020 09:14:23: #2 alternative fragment length(s) may be 215 bps INFO @ Tue, 16 Jun 2020 09:14:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495088/SRX495088.10_model.r INFO @ Tue, 16 Jun 2020 09:14:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:14:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:14:27: 2000000 INFO @ Tue, 16 Jun 2020 09:14:32: 3000000 INFO @ Tue, 16 Jun 2020 09:14:37: 4000000 INFO @ Tue, 16 Jun 2020 09:14:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:14:41: 5000000 INFO @ Tue, 16 Jun 2020 09:14:46: 6000000 INFO @ Tue, 16 Jun 2020 09:14:47: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:14:47: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:14:47: #1 total tags in treatment: 6416818 INFO @ Tue, 16 Jun 2020 09:14:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:14:47: #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 09:14:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495088/SRX495088.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:14:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495088/SRX495088.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:14:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495088/SRX495088.10_summits.bed INFO @ Tue, 16 Jun 2020 09:14:48: #1 tags after filtering in treatment: 6416818 INFO @ Tue, 16 Jun 2020 09:14:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:14:48: #1 finished! INFO @ Tue, 16 Jun 2020 09:14:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:14:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:14:48: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1869 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:14:48: #2 number of paired peaks: 1384 INFO @ Tue, 16 Jun 2020 09:14:48: start model_add_line... INFO @ Tue, 16 Jun 2020 09:14:48: start X-correlation... INFO @ Tue, 16 Jun 2020 09:14:48: end of X-cor INFO @ Tue, 16 Jun 2020 09:14:48: #2 finished! INFO @ Tue, 16 Jun 2020 09:14:48: #2 predicted fragment length is 215 bps INFO @ Tue, 16 Jun 2020 09:14:48: #2 alternative fragment length(s) may be 215 bps INFO @ Tue, 16 Jun 2020 09:14:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495088/SRX495088.20_model.r INFO @ Tue, 16 Jun 2020 09:14:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:14:48: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:15:06: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:15:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495088/SRX495088.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:15:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495088/SRX495088.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:15:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495088/SRX495088.20_summits.bed INFO @ Tue, 16 Jun 2020 09:15:13: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (990 records, 4 fields): 4 millis CompletedMACS2peakCalling