Job ID = 16435016 SRX = SRX13110313 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T01:31:02 prefetch.2.10.7: 1) Downloading 'SRR16917983'... 2022-08-02T01:31:02 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T01:31:06 prefetch.2.10.7: HTTPS download succeed 2022-08-02T01:31:06 prefetch.2.10.7: 'SRR16917983' is valid 2022-08-02T01:31:06 prefetch.2.10.7: 1) 'SRR16917983' was downloaded successfully 2022-08-02T01:31:06 prefetch.2.10.7: 'SRR16917983' has 0 unresolved dependencies Read 7352008 spots for SRR16917983/SRR16917983.sra Written 7352008 spots for SRR16917983/SRR16917983.sra fastq に変換しました。 bowtie でマッピング中... Your job 16435138 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:16 7352008 reads; of these: 7352008 (100.00%) were unpaired; of these: 1602763 (21.80%) aligned 0 times 5098907 (69.35%) aligned exactly 1 time 650338 (8.85%) aligned >1 times 78.20% overall alignment rate Time searching: 00:02:16 Overall time: 00:02:16 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] 2081161 / 5749245 = 0.3620 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:35:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110313/SRX13110313.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110313/SRX13110313.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110313/SRX13110313.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110313/SRX13110313.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, 02 Aug 2022 10:35:51: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:35:51: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:35:59: 1000000 INFO @ Tue, 02 Aug 2022 10:36:06: 2000000 INFO @ Tue, 02 Aug 2022 10:36:14: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:36:19: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:36:19: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:36:19: #1 total tags in treatment: 3668084 INFO @ Tue, 02 Aug 2022 10:36:19: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:36:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:36:19: #1 tags after filtering in treatment: 3668084 INFO @ Tue, 02 Aug 2022 10:36:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:36:19: #1 finished! INFO @ Tue, 02 Aug 2022 10:36:19: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:36:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:36:19: #2 number of paired peaks: 1401 INFO @ Tue, 02 Aug 2022 10:36:19: start model_add_line... INFO @ Tue, 02 Aug 2022 10:36:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110313/SRX13110313.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110313/SRX13110313.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110313/SRX13110313.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110313/SRX13110313.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, 02 Aug 2022 10:36:19: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:36:19: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:36:19: start X-correlation... INFO @ Tue, 02 Aug 2022 10:36:20: end of X-cor INFO @ Tue, 02 Aug 2022 10:36:20: #2 finished! INFO @ Tue, 02 Aug 2022 10:36:20: #2 predicted fragment length is 220 bps INFO @ Tue, 02 Aug 2022 10:36:20: #2 alternative fragment length(s) may be 220 bps INFO @ Tue, 02 Aug 2022 10:36:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110313/SRX13110313.05_model.r INFO @ Tue, 02 Aug 2022 10:36:20: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:36:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:36:27: 1000000 INFO @ Tue, 02 Aug 2022 10:36:29: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:36:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110313/SRX13110313.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:36:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110313/SRX13110313.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:36:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110313/SRX13110313.05_summits.bed INFO @ Tue, 02 Aug 2022 10:36:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1856 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:36:35: 2000000 INFO @ Tue, 02 Aug 2022 10:36:43: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:36:48: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:36:48: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:36:48: #1 total tags in treatment: 3668084 INFO @ Tue, 02 Aug 2022 10:36:48: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:36:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:36:48: #1 tags after filtering in treatment: 3668084 INFO @ Tue, 02 Aug 2022 10:36:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:36:48: #1 finished! INFO @ Tue, 02 Aug 2022 10:36:48: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:36:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:36:48: #2 number of paired peaks: 1401 INFO @ Tue, 02 Aug 2022 10:36:48: start model_add_line... INFO @ Tue, 02 Aug 2022 10:36:48: start X-correlation... INFO @ Tue, 02 Aug 2022 10:36:48: end of X-cor INFO @ Tue, 02 Aug 2022 10:36:48: #2 finished! INFO @ Tue, 02 Aug 2022 10:36:48: #2 predicted fragment length is 220 bps INFO @ Tue, 02 Aug 2022 10:36:48: #2 alternative fragment length(s) may be 220 bps INFO @ Tue, 02 Aug 2022 10:36:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110313/SRX13110313.10_model.r INFO @ Tue, 02 Aug 2022 10:36:48: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:36:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:36:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110313/SRX13110313.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110313/SRX13110313.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110313/SRX13110313.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110313/SRX13110313.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, 02 Aug 2022 10:36:49: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:36:49: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:36:56: 1000000 INFO @ Tue, 02 Aug 2022 10:36:58: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:37:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110313/SRX13110313.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:37:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110313/SRX13110313.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:37:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110313/SRX13110313.10_summits.bed INFO @ Tue, 02 Aug 2022 10:37:02: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (727 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:37:03: 2000000 INFO @ Tue, 02 Aug 2022 10:37:10: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:37:15: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:37:15: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:37:15: #1 total tags in treatment: 3668084 INFO @ Tue, 02 Aug 2022 10:37:15: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:37:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:37:15: #1 tags after filtering in treatment: 3668084 INFO @ Tue, 02 Aug 2022 10:37:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:37:15: #1 finished! INFO @ Tue, 02 Aug 2022 10:37:15: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:37:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:37:15: #2 number of paired peaks: 1401 INFO @ Tue, 02 Aug 2022 10:37:15: start model_add_line... INFO @ Tue, 02 Aug 2022 10:37:15: start X-correlation... INFO @ Tue, 02 Aug 2022 10:37:15: end of X-cor INFO @ Tue, 02 Aug 2022 10:37:15: #2 finished! INFO @ Tue, 02 Aug 2022 10:37:15: #2 predicted fragment length is 220 bps INFO @ Tue, 02 Aug 2022 10:37:15: #2 alternative fragment length(s) may be 220 bps INFO @ Tue, 02 Aug 2022 10:37:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110313/SRX13110313.20_model.r INFO @ Tue, 02 Aug 2022 10:37:15: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:37:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:37:25: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:37:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110313/SRX13110313.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:37:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110313/SRX13110313.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:37:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110313/SRX13110313.20_summits.bed INFO @ Tue, 02 Aug 2022 10:37:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (243 records, 4 fields): 16 millis CompletedMACS2peakCalling