Job ID = 6368078 SRX = SRX466541 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:56:13 prefetch.2.10.7: 1) Downloading 'SRR1163607'... 2020-06-15T23:56:13 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:57:35 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:57:36 prefetch.2.10.7: 'SRR1163607' is valid 2020-06-15T23:57:36 prefetch.2.10.7: 1) 'SRR1163607' was downloaded successfully Read 9182496 spots for SRR1163607/SRR1163607.sra Written 9182496 spots for SRR1163607/SRR1163607.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: 00:01:41 9182496 reads; of these: 9182496 (100.00%) were unpaired; of these: 486931 (5.30%) aligned 0 times 7902635 (86.06%) aligned exactly 1 time 792930 (8.64%) aligned >1 times 94.70% overall alignment rate Time searching: 00:01:41 Overall time: 00:01:41 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] 6574887 / 8695565 = 0.7561 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 09:01:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466541/SRX466541.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466541/SRX466541.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466541/SRX466541.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466541/SRX466541.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 09:01:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:01:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:01:44: 1000000 INFO @ Tue, 16 Jun 2020 09:01:50: 2000000 INFO @ Tue, 16 Jun 2020 09:01:50: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:01:50: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:01:50: #1 total tags in treatment: 2120678 INFO @ Tue, 16 Jun 2020 09:01:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:01:50: #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 09:01:50: #1 tags after filtering in treatment: 2120678 INFO @ Tue, 16 Jun 2020 09:01:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:01:50: #1 finished! INFO @ Tue, 16 Jun 2020 09:01:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:01:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:01:51: #2 number of paired peaks: 6663 INFO @ Tue, 16 Jun 2020 09:01:51: start model_add_line... INFO @ Tue, 16 Jun 2020 09:01:51: start X-correlation... INFO @ Tue, 16 Jun 2020 09:01:51: end of X-cor INFO @ Tue, 16 Jun 2020 09:01:51: #2 finished! INFO @ Tue, 16 Jun 2020 09:01:51: #2 predicted fragment length is 308 bps INFO @ Tue, 16 Jun 2020 09:01:51: #2 alternative fragment length(s) may be 308 bps INFO @ Tue, 16 Jun 2020 09:01:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466541/SRX466541.05_model.r INFO @ Tue, 16 Jun 2020 09:01:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:01:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:01:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:02:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466541/SRX466541.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:02:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466541/SRX466541.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:02:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466541/SRX466541.05_summits.bed INFO @ Tue, 16 Jun 2020 09:02:02: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4111 records, 4 fields): 5 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 09:02:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466541/SRX466541.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466541/SRX466541.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466541/SRX466541.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466541/SRX466541.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 09:02:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:02:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:02:14: 1000000 INFO @ Tue, 16 Jun 2020 09:02:20: 2000000 INFO @ Tue, 16 Jun 2020 09:02:21: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:02:21: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:02:21: #1 total tags in treatment: 2120678 INFO @ Tue, 16 Jun 2020 09:02:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:02:21: #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 09:02:21: #1 tags after filtering in treatment: 2120678 INFO @ Tue, 16 Jun 2020 09:02:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:02:21: #1 finished! INFO @ Tue, 16 Jun 2020 09:02:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:02:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:02:21: #2 number of paired peaks: 6663 INFO @ Tue, 16 Jun 2020 09:02:21: start model_add_line... INFO @ Tue, 16 Jun 2020 09:02:21: start X-correlation... INFO @ Tue, 16 Jun 2020 09:02:21: end of X-cor INFO @ Tue, 16 Jun 2020 09:02:21: #2 finished! INFO @ Tue, 16 Jun 2020 09:02:21: #2 predicted fragment length is 308 bps INFO @ Tue, 16 Jun 2020 09:02:21: #2 alternative fragment length(s) may be 308 bps INFO @ Tue, 16 Jun 2020 09:02:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466541/SRX466541.10_model.r INFO @ Tue, 16 Jun 2020 09:02:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:02:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:02:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:02:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466541/SRX466541.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:02:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466541/SRX466541.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:02:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466541/SRX466541.10_summits.bed INFO @ Tue, 16 Jun 2020 09:02:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3476 records, 4 fields): 5 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 09:02:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466541/SRX466541.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466541/SRX466541.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466541/SRX466541.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466541/SRX466541.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 09:02:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:02:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:02:44: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:02:50: 2000000 INFO @ Tue, 16 Jun 2020 09:02:51: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:02:51: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:02:51: #1 total tags in treatment: 2120678 INFO @ Tue, 16 Jun 2020 09:02:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:02:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:02:51: #1 tags after filtering in treatment: 2120678 INFO @ Tue, 16 Jun 2020 09:02:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:02:51: #1 finished! INFO @ Tue, 16 Jun 2020 09:02:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:02:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:02:51: #2 number of paired peaks: 6663 INFO @ Tue, 16 Jun 2020 09:02:51: start model_add_line... INFO @ Tue, 16 Jun 2020 09:02:51: start X-correlation... INFO @ Tue, 16 Jun 2020 09:02:51: end of X-cor INFO @ Tue, 16 Jun 2020 09:02:51: #2 finished! INFO @ Tue, 16 Jun 2020 09:02:51: #2 predicted fragment length is 308 bps INFO @ Tue, 16 Jun 2020 09:02:51: #2 alternative fragment length(s) may be 308 bps INFO @ Tue, 16 Jun 2020 09:02:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466541/SRX466541.20_model.r INFO @ Tue, 16 Jun 2020 09:02:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:02:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:02:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:03:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466541/SRX466541.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:03:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466541/SRX466541.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:03:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466541/SRX466541.20_summits.bed INFO @ Tue, 16 Jun 2020 09:03:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2655 records, 4 fields): 4 millis CompletedMACS2peakCalling