Job ID = 6366293 SRX = SRX1078717 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:35:21 prefetch.2.10.7: 1) Downloading 'SRR2084324'... 2020-06-15T22:35:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:36:27 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:36:28 prefetch.2.10.7: 'SRR2084324' is valid 2020-06-15T22:36:28 prefetch.2.10.7: 1) 'SRR2084324' was downloaded successfully Read 11390104 spots for SRR2084324/SRR2084324.sra Written 11390104 spots for SRR2084324/SRR2084324.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: 00:02:35 11390104 reads; of these: 11390104 (100.00%) were unpaired; of these: 888618 (7.80%) aligned 0 times 8747781 (76.80%) aligned exactly 1 time 1753705 (15.40%) aligned >1 times 92.20% overall alignment rate Time searching: 00:02:35 Overall time: 00:02:35 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_sort_core] merging from 8 files... [bam_rmdupse_core] 4739995 / 10501486 = 0.4514 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 07:42:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078717/SRX1078717.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078717/SRX1078717.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078717/SRX1078717.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078717/SRX1078717.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 07:42:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:42:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:42:35: 1000000 INFO @ Tue, 16 Jun 2020 07:42:41: 2000000 INFO @ Tue, 16 Jun 2020 07:42:47: 3000000 INFO @ Tue, 16 Jun 2020 07:42:53: 4000000 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 07:42:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078717/SRX1078717.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078717/SRX1078717.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078717/SRX1078717.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078717/SRX1078717.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 07:42:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:42:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:43:00: 5000000 INFO @ Tue, 16 Jun 2020 07:43:06: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:43:06: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:43:06: #1 total tags in treatment: 5761491 INFO @ Tue, 16 Jun 2020 07:43:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:43:06: #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 07:43:06: #1 tags after filtering in treatment: 5761491 INFO @ Tue, 16 Jun 2020 07:43:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:43:06: #1 finished! INFO @ Tue, 16 Jun 2020 07:43:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:43:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:43:06: #2 number of paired peaks: 1269 INFO @ Tue, 16 Jun 2020 07:43:06: start model_add_line... INFO @ Tue, 16 Jun 2020 07:43:06: start X-correlation... INFO @ Tue, 16 Jun 2020 07:43:06: end of X-cor INFO @ Tue, 16 Jun 2020 07:43:06: #2 finished! INFO @ Tue, 16 Jun 2020 07:43:06: #2 predicted fragment length is 223 bps INFO @ Tue, 16 Jun 2020 07:43:06: #2 alternative fragment length(s) may be 223 bps INFO @ Tue, 16 Jun 2020 07:43:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078717/SRX1078717.05_model.r INFO @ Tue, 16 Jun 2020 07:43:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:43:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:43:07: 1000000 INFO @ Tue, 16 Jun 2020 07:43:14: 2000000 INFO @ Tue, 16 Jun 2020 07:43:20: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:43:21: 3000000 INFO @ Tue, 16 Jun 2020 07:43:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1078717/SRX1078717.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:43:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1078717/SRX1078717.05_peaks.narrowPeak BedGraph に変換中... INFO @ Tue, 16 Jun 2020 07:43:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1078717/SRX1078717.05_summits.bed INFO @ Tue, 16 Jun 2020 07:43:27: Done! 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 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4196 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:43:28: 4000000 INFO @ Tue, 16 Jun 2020 07:43:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078717/SRX1078717.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078717/SRX1078717.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078717/SRX1078717.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078717/SRX1078717.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 07:43:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:43:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:43:36: 5000000 INFO @ Tue, 16 Jun 2020 07:43:37: 1000000 INFO @ Tue, 16 Jun 2020 07:43:43: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:43:43: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:43:43: #1 total tags in treatment: 5761491 INFO @ Tue, 16 Jun 2020 07:43:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:43:43: #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 07:43:43: #1 tags after filtering in treatment: 5761491 INFO @ Tue, 16 Jun 2020 07:43:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:43:43: #1 finished! INFO @ Tue, 16 Jun 2020 07:43:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:43:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:43:43: #2 number of paired peaks: 1269 INFO @ Tue, 16 Jun 2020 07:43:43: start model_add_line... INFO @ Tue, 16 Jun 2020 07:43:43: start X-correlation... INFO @ Tue, 16 Jun 2020 07:43:43: end of X-cor INFO @ Tue, 16 Jun 2020 07:43:43: #2 finished! INFO @ Tue, 16 Jun 2020 07:43:43: #2 predicted fragment length is 223 bps INFO @ Tue, 16 Jun 2020 07:43:43: #2 alternative fragment length(s) may be 223 bps INFO @ Tue, 16 Jun 2020 07:43:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078717/SRX1078717.10_model.r INFO @ Tue, 16 Jun 2020 07:43:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:43:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:43:44: 2000000 INFO @ Tue, 16 Jun 2020 07:43:51: 3000000 INFO @ Tue, 16 Jun 2020 07:43:57: 4000000 INFO @ Tue, 16 Jun 2020 07:43:59: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:44:03: 5000000 INFO @ Tue, 16 Jun 2020 07:44:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1078717/SRX1078717.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:44:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1078717/SRX1078717.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:44:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1078717/SRX1078717.10_summits.bed INFO @ Tue, 16 Jun 2020 07:44:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2355 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:44:08: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:44:08: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:44:08: #1 total tags in treatment: 5761491 INFO @ Tue, 16 Jun 2020 07:44:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:44:08: #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 07:44:08: #1 tags after filtering in treatment: 5761491 INFO @ Tue, 16 Jun 2020 07:44:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:44:08: #1 finished! INFO @ Tue, 16 Jun 2020 07:44:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:44:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:44:09: #2 number of paired peaks: 1269 INFO @ Tue, 16 Jun 2020 07:44:09: start model_add_line... INFO @ Tue, 16 Jun 2020 07:44:09: start X-correlation... INFO @ Tue, 16 Jun 2020 07:44:09: end of X-cor INFO @ Tue, 16 Jun 2020 07:44:09: #2 finished! INFO @ Tue, 16 Jun 2020 07:44:09: #2 predicted fragment length is 223 bps INFO @ Tue, 16 Jun 2020 07:44:09: #2 alternative fragment length(s) may be 223 bps INFO @ Tue, 16 Jun 2020 07:44:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078717/SRX1078717.20_model.r INFO @ Tue, 16 Jun 2020 07:44:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:44:09: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:44:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:44:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1078717/SRX1078717.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:44:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1078717/SRX1078717.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:44:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1078717/SRX1078717.20_summits.bed INFO @ Tue, 16 Jun 2020 07:44:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1037 records, 4 fields): 3 millis CompletedMACS2peakCalling