Job ID = 6365939 SRX = SRX043872 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:34:36 prefetch.2.10.7: 1) Downloading 'SRR107340'... 2020-06-15T22:34:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:35:10 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:35:10 prefetch.2.10.7: 'SRR107340' is valid 2020-06-15T22:35:10 prefetch.2.10.7: 1) 'SRR107340' was downloaded successfully Read 3046025 spots for SRR107340/SRR107340.sra Written 3046025 spots for SRR107340/SRR107340.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: 00:00:21 3046025 reads; of these: 3046025 (100.00%) were unpaired; of these: 1540358 (50.57%) aligned 0 times 1360814 (44.68%) aligned exactly 1 time 144853 (4.76%) aligned >1 times 49.43% overall alignment rate Time searching: 00:00:21 Overall time: 00:00:21 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] 126339 / 1505667 = 0.0839 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 07:36:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043872/SRX043872.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043872/SRX043872.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043872/SRX043872.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043872/SRX043872.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 07:36:36: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:36:36: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:36:42: 1000000 INFO @ Tue, 16 Jun 2020 07:36:44: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:36:44: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:36:44: #1 total tags in treatment: 1379328 INFO @ Tue, 16 Jun 2020 07:36:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:36:44: #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 07:36:44: #1 tags after filtering in treatment: 1379328 INFO @ Tue, 16 Jun 2020 07:36:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:36:44: #1 finished! INFO @ Tue, 16 Jun 2020 07:36:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:36:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:36:44: #2 number of paired peaks: 2862 INFO @ Tue, 16 Jun 2020 07:36:44: start model_add_line... INFO @ Tue, 16 Jun 2020 07:36:44: start X-correlation... INFO @ Tue, 16 Jun 2020 07:36:44: end of X-cor INFO @ Tue, 16 Jun 2020 07:36:44: #2 finished! INFO @ Tue, 16 Jun 2020 07:36:44: #2 predicted fragment length is 137 bps INFO @ Tue, 16 Jun 2020 07:36:44: #2 alternative fragment length(s) may be 137,565 bps INFO @ Tue, 16 Jun 2020 07:36:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043872/SRX043872.05_model.r INFO @ Tue, 16 Jun 2020 07:36:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:36:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:36:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:36:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043872/SRX043872.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:36:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043872/SRX043872.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:36:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043872/SRX043872.05_summits.bed INFO @ Tue, 16 Jun 2020 07:36:50: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1391 records, 4 fields): 3 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 07:37:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043872/SRX043872.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043872/SRX043872.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043872/SRX043872.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043872/SRX043872.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 07:37:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:37:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:37:11: 1000000 INFO @ Tue, 16 Jun 2020 07:37:13: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:37:13: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:37:13: #1 total tags in treatment: 1379328 INFO @ Tue, 16 Jun 2020 07:37:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:37:13: #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 07:37:13: #1 tags after filtering in treatment: 1379328 INFO @ Tue, 16 Jun 2020 07:37:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:37:13: #1 finished! INFO @ Tue, 16 Jun 2020 07:37:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:37:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:37:14: #2 number of paired peaks: 2862 INFO @ Tue, 16 Jun 2020 07:37:14: start model_add_line... INFO @ Tue, 16 Jun 2020 07:37:14: start X-correlation... INFO @ Tue, 16 Jun 2020 07:37:14: end of X-cor INFO @ Tue, 16 Jun 2020 07:37:14: #2 finished! INFO @ Tue, 16 Jun 2020 07:37:14: #2 predicted fragment length is 137 bps INFO @ Tue, 16 Jun 2020 07:37:14: #2 alternative fragment length(s) may be 137,565 bps INFO @ Tue, 16 Jun 2020 07:37:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043872/SRX043872.10_model.r INFO @ Tue, 16 Jun 2020 07:37:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:37:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:37:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:37:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043872/SRX043872.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:37:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043872/SRX043872.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:37:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043872/SRX043872.10_summits.bed INFO @ Tue, 16 Jun 2020 07:37:19: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (487 records, 4 fields): 2 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 07:37:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043872/SRX043872.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043872/SRX043872.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043872/SRX043872.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043872/SRX043872.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 07:37:36: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:37:36: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:37:41: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:37:43: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:37:43: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:37:43: #1 total tags in treatment: 1379328 INFO @ Tue, 16 Jun 2020 07:37:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:37:43: #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 07:37:43: #1 tags after filtering in treatment: 1379328 INFO @ Tue, 16 Jun 2020 07:37:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:37:43: #1 finished! INFO @ Tue, 16 Jun 2020 07:37:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:37:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:37:44: #2 number of paired peaks: 2862 INFO @ Tue, 16 Jun 2020 07:37:44: start model_add_line... INFO @ Tue, 16 Jun 2020 07:37:44: start X-correlation... INFO @ Tue, 16 Jun 2020 07:37:44: end of X-cor INFO @ Tue, 16 Jun 2020 07:37:44: #2 finished! INFO @ Tue, 16 Jun 2020 07:37:44: #2 predicted fragment length is 137 bps INFO @ Tue, 16 Jun 2020 07:37:44: #2 alternative fragment length(s) may be 137,565 bps INFO @ Tue, 16 Jun 2020 07:37:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043872/SRX043872.20_model.r INFO @ Tue, 16 Jun 2020 07:37:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:37:44: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:37:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:37:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043872/SRX043872.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:37:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043872/SRX043872.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:37:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043872/SRX043872.20_summits.bed INFO @ Tue, 16 Jun 2020 07:37:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (134 records, 4 fields): 1 millis CompletedMACS2peakCalling