Job ID = 6368656 SRX = SRX529216 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:21:51 prefetch.2.10.7: 1) Downloading 'SRR1265820'... 2020-06-16T00:21:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:22:44 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:22:44 prefetch.2.10.7: 'SRR1265820' is valid 2020-06-16T00:22:44 prefetch.2.10.7: 1) 'SRR1265820' was downloaded successfully Read 14099125 spots for SRR1265820/SRR1265820.sra Written 14099125 spots for SRR1265820/SRR1265820.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 14099125 reads; of these: 14099125 (100.00%) were unpaired; of these: 4725149 (33.51%) aligned 0 times 6841759 (48.53%) aligned exactly 1 time 2532217 (17.96%) aligned >1 times 66.49% 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] 1263712 / 9373976 = 0.1348 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 09:27:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529216/SRX529216.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529216/SRX529216.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529216/SRX529216.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529216/SRX529216.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 09:27:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:27:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:27:21: 1000000 INFO @ Tue, 16 Jun 2020 09:27:27: 2000000 INFO @ Tue, 16 Jun 2020 09:27:31: 3000000 INFO @ Tue, 16 Jun 2020 09:27:36: 4000000 INFO @ Tue, 16 Jun 2020 09:27:41: 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 09:27:46: 6000000 INFO @ Tue, 16 Jun 2020 09:27:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529216/SRX529216.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529216/SRX529216.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529216/SRX529216.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529216/SRX529216.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 09:27:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:27:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:27:52: 7000000 INFO @ Tue, 16 Jun 2020 09:27:52: 1000000 INFO @ Tue, 16 Jun 2020 09:27:57: 8000000 INFO @ Tue, 16 Jun 2020 09:27:58: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 09:27:58: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 09:27:58: #1 total tags in treatment: 8110264 INFO @ Tue, 16 Jun 2020 09:27:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:27:58: #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 09:27:58: 2000000 INFO @ Tue, 16 Jun 2020 09:27:58: #1 tags after filtering in treatment: 8110264 INFO @ Tue, 16 Jun 2020 09:27:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:27:58: #1 finished! INFO @ Tue, 16 Jun 2020 09:27:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:27:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:27:58: #2 number of paired peaks: 1615 INFO @ Tue, 16 Jun 2020 09:27:58: start model_add_line... INFO @ Tue, 16 Jun 2020 09:27:58: start X-correlation... INFO @ Tue, 16 Jun 2020 09:27:59: end of X-cor INFO @ Tue, 16 Jun 2020 09:27:59: #2 finished! INFO @ Tue, 16 Jun 2020 09:27:59: #2 predicted fragment length is 128 bps INFO @ Tue, 16 Jun 2020 09:27:59: #2 alternative fragment length(s) may be 2,128,140 bps INFO @ Tue, 16 Jun 2020 09:27:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529216/SRX529216.05_model.r INFO @ Tue, 16 Jun 2020 09:27:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:27:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:28:03: 3000000 INFO @ Tue, 16 Jun 2020 09:28:08: 4000000 INFO @ Tue, 16 Jun 2020 09:28:13: 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 09:28:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529216/SRX529216.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529216/SRX529216.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529216/SRX529216.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529216/SRX529216.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 09:28:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:28:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:28:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:28:19: 6000000 INFO @ Tue, 16 Jun 2020 09:28:22: 1000000 INFO @ Tue, 16 Jun 2020 09:28:25: 7000000 INFO @ Tue, 16 Jun 2020 09:28:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529216/SRX529216.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:28:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529216/SRX529216.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:28:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529216/SRX529216.05_summits.bed INFO @ Tue, 16 Jun 2020 09:28:28: Done! INFO @ Tue, 16 Jun 2020 09:28:28: 2000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2459 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:28:31: 8000000 INFO @ Tue, 16 Jun 2020 09:28:31: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 09:28:31: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 09:28:31: #1 total tags in treatment: 8110264 INFO @ Tue, 16 Jun 2020 09:28:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:28:31: #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 09:28:31: #1 tags after filtering in treatment: 8110264 INFO @ Tue, 16 Jun 2020 09:28:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:28:31: #1 finished! INFO @ Tue, 16 Jun 2020 09:28:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:28:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:28:32: #2 number of paired peaks: 1615 INFO @ Tue, 16 Jun 2020 09:28:32: start model_add_line... INFO @ Tue, 16 Jun 2020 09:28:32: start X-correlation... INFO @ Tue, 16 Jun 2020 09:28:32: end of X-cor INFO @ Tue, 16 Jun 2020 09:28:32: #2 finished! INFO @ Tue, 16 Jun 2020 09:28:32: #2 predicted fragment length is 128 bps INFO @ Tue, 16 Jun 2020 09:28:32: #2 alternative fragment length(s) may be 2,128,140 bps INFO @ Tue, 16 Jun 2020 09:28:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529216/SRX529216.10_model.r INFO @ Tue, 16 Jun 2020 09:28:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:28:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:28:34: 3000000 INFO @ Tue, 16 Jun 2020 09:28:40: 4000000 INFO @ Tue, 16 Jun 2020 09:28:46: 5000000 INFO @ Tue, 16 Jun 2020 09:28:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:28:52: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:28:58: 7000000 INFO @ Tue, 16 Jun 2020 09:29:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529216/SRX529216.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:29:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529216/SRX529216.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:29:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529216/SRX529216.10_summits.bed INFO @ Tue, 16 Jun 2020 09:29:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (756 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:29:03: 8000000 INFO @ Tue, 16 Jun 2020 09:29:04: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 09:29:04: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 09:29:04: #1 total tags in treatment: 8110264 INFO @ Tue, 16 Jun 2020 09:29:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:29:04: #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 09:29:04: #1 tags after filtering in treatment: 8110264 INFO @ Tue, 16 Jun 2020 09:29:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:29:04: #1 finished! INFO @ Tue, 16 Jun 2020 09:29:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:29:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:29:05: #2 number of paired peaks: 1615 INFO @ Tue, 16 Jun 2020 09:29:05: start model_add_line... INFO @ Tue, 16 Jun 2020 09:29:05: start X-correlation... INFO @ Tue, 16 Jun 2020 09:29:05: end of X-cor INFO @ Tue, 16 Jun 2020 09:29:05: #2 finished! INFO @ Tue, 16 Jun 2020 09:29:05: #2 predicted fragment length is 128 bps INFO @ Tue, 16 Jun 2020 09:29:05: #2 alternative fragment length(s) may be 2,128,140 bps INFO @ Tue, 16 Jun 2020 09:29:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529216/SRX529216.20_model.r INFO @ Tue, 16 Jun 2020 09:29:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:29:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:29:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:29:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529216/SRX529216.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:29:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529216/SRX529216.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:29:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529216/SRX529216.20_summits.bed INFO @ Tue, 16 Jun 2020 09:29:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (223 records, 4 fields): 1 millis CompletedMACS2peakCalling