Job ID = 6507960 SRX = SRX495119 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:58:56 prefetch.2.10.7: 1) Downloading 'SRR1198651'... 2020-06-26T13:58:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:59:53 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:59:53 prefetch.2.10.7: 'SRR1198651' is valid 2020-06-26T13:59:53 prefetch.2.10.7: 1) 'SRR1198651' was downloaded successfully Read 8982852 spots for SRR1198651/SRR1198651.sra Written 8982852 spots for SRR1198651/SRR1198651.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: 00:01:18 8982852 reads; of these: 8982852 (100.00%) were unpaired; of these: 1010086 (11.24%) aligned 0 times 6430028 (71.58%) aligned exactly 1 time 1542738 (17.17%) aligned >1 times 88.76% overall alignment rate Time searching: 00:01:18 Overall time: 00:01:18 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] 2269335 / 7972766 = 0.2846 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 @ Fri, 26 Jun 2020 23:03:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495119/SRX495119.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495119/SRX495119.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495119/SRX495119.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495119/SRX495119.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 @ Fri, 26 Jun 2020 23:03:37: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:03:37: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:03:42: 1000000 INFO @ Fri, 26 Jun 2020 23:03:48: 2000000 INFO @ Fri, 26 Jun 2020 23:03:53: 3000000 INFO @ Fri, 26 Jun 2020 23:03:59: 4000000 INFO @ Fri, 26 Jun 2020 23:04:04: 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 @ Fri, 26 Jun 2020 23:04:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495119/SRX495119.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495119/SRX495119.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495119/SRX495119.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495119/SRX495119.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 @ Fri, 26 Jun 2020 23:04:07: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:04:07: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:04:07: #1 tag size is determined as 29 bps INFO @ Fri, 26 Jun 2020 23:04:07: #1 tag size = 29 INFO @ Fri, 26 Jun 2020 23:04:07: #1 total tags in treatment: 5703431 INFO @ Fri, 26 Jun 2020 23:04:07: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:04:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:04:08: #1 tags after filtering in treatment: 5703431 INFO @ Fri, 26 Jun 2020 23:04:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:04:08: #1 finished! INFO @ Fri, 26 Jun 2020 23:04:08: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:04:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:04:08: #2 number of paired peaks: 1923 INFO @ Fri, 26 Jun 2020 23:04:08: start model_add_line... INFO @ Fri, 26 Jun 2020 23:04:08: start X-correlation... INFO @ Fri, 26 Jun 2020 23:04:08: end of X-cor INFO @ Fri, 26 Jun 2020 23:04:08: #2 finished! INFO @ Fri, 26 Jun 2020 23:04:08: #2 predicted fragment length is 194 bps INFO @ Fri, 26 Jun 2020 23:04:08: #2 alternative fragment length(s) may be 194 bps INFO @ Fri, 26 Jun 2020 23:04:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495119/SRX495119.05_model.r INFO @ Fri, 26 Jun 2020 23:04:08: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:04:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:04:14: 1000000 INFO @ Fri, 26 Jun 2020 23:04:21: 2000000 INFO @ Fri, 26 Jun 2020 23:04:26: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:04:28: 3000000 INFO @ Fri, 26 Jun 2020 23:04:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495119/SRX495119.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:04:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495119/SRX495119.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:04:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495119/SRX495119.05_summits.bed INFO @ Fri, 26 Jun 2020 23:04:35: Done! BedGraph に変換中... pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2928 records, 4 fields): 5 millis 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 CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:04:35: 4000000 INFO @ Fri, 26 Jun 2020 23:04:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495119/SRX495119.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495119/SRX495119.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495119/SRX495119.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495119/SRX495119.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 @ Fri, 26 Jun 2020 23:04:37: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:04:37: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:04:43: 5000000 INFO @ Fri, 26 Jun 2020 23:04:43: 1000000 INFO @ Fri, 26 Jun 2020 23:04:47: #1 tag size is determined as 29 bps INFO @ Fri, 26 Jun 2020 23:04:47: #1 tag size = 29 INFO @ Fri, 26 Jun 2020 23:04:47: #1 total tags in treatment: 5703431 INFO @ Fri, 26 Jun 2020 23:04:47: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:04:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:04:47: #1 tags after filtering in treatment: 5703431 INFO @ Fri, 26 Jun 2020 23:04:47: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:04:47: #1 finished! INFO @ Fri, 26 Jun 2020 23:04:47: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:04:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:04:48: #2 number of paired peaks: 1923 INFO @ Fri, 26 Jun 2020 23:04:48: start model_add_line... INFO @ Fri, 26 Jun 2020 23:04:48: start X-correlation... INFO @ Fri, 26 Jun 2020 23:04:48: end of X-cor INFO @ Fri, 26 Jun 2020 23:04:48: #2 finished! INFO @ Fri, 26 Jun 2020 23:04:48: #2 predicted fragment length is 194 bps INFO @ Fri, 26 Jun 2020 23:04:48: #2 alternative fragment length(s) may be 194 bps INFO @ Fri, 26 Jun 2020 23:04:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495119/SRX495119.10_model.r INFO @ Fri, 26 Jun 2020 23:04:48: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:04:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:04:49: 2000000 INFO @ Fri, 26 Jun 2020 23:04:54: 3000000 INFO @ Fri, 26 Jun 2020 23:05:00: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:05:06: 5000000 INFO @ Fri, 26 Jun 2020 23:05:07: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:05:09: #1 tag size is determined as 29 bps INFO @ Fri, 26 Jun 2020 23:05:09: #1 tag size = 29 INFO @ Fri, 26 Jun 2020 23:05:09: #1 total tags in treatment: 5703431 INFO @ Fri, 26 Jun 2020 23:05:09: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:05:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:05:09: #1 tags after filtering in treatment: 5703431 INFO @ Fri, 26 Jun 2020 23:05:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:05:09: #1 finished! INFO @ Fri, 26 Jun 2020 23:05:09: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:05:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:05:10: #2 number of paired peaks: 1923 INFO @ Fri, 26 Jun 2020 23:05:10: start model_add_line... INFO @ Fri, 26 Jun 2020 23:05:10: start X-correlation... INFO @ Fri, 26 Jun 2020 23:05:10: end of X-cor INFO @ Fri, 26 Jun 2020 23:05:10: #2 finished! INFO @ Fri, 26 Jun 2020 23:05:10: #2 predicted fragment length is 194 bps INFO @ Fri, 26 Jun 2020 23:05:10: #2 alternative fragment length(s) may be 194 bps INFO @ Fri, 26 Jun 2020 23:05:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495119/SRX495119.20_model.r INFO @ Fri, 26 Jun 2020 23:05:10: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:05:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:05:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495119/SRX495119.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:05:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495119/SRX495119.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:05:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495119/SRX495119.10_summits.bed INFO @ Fri, 26 Jun 2020 23:05:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1219 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:05:26: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:05:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495119/SRX495119.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:05:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495119/SRX495119.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:05:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495119/SRX495119.20_summits.bed INFO @ Fri, 26 Jun 2020 23:05:34: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (469 records, 4 fields): 2 millis CompletedMACS2peakCalling