Job ID = 16435024 SRX = SRX13110314 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T01:32:47 prefetch.2.10.7: 1) Downloading 'SRR16917984'... 2022-08-02T01:32:47 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T01:33:40 prefetch.2.10.7: HTTPS download succeed 2022-08-02T01:33:41 prefetch.2.10.7: 'SRR16917984' is valid 2022-08-02T01:33:41 prefetch.2.10.7: 1) 'SRR16917984' was downloaded successfully 2022-08-02T01:33:41 prefetch.2.10.7: 'SRR16917984' has 0 unresolved dependencies Read 18087252 spots for SRR16917984/SRR16917984.sra Written 18087252 spots for SRR16917984/SRR16917984.sra fastq に変換しました。 bowtie でマッピング中... Your job 16435508 ("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: 00:05:07 18087252 reads; of these: 18087252 (100.00%) were unpaired; of these: 5141137 (28.42%) aligned 0 times 11283996 (62.39%) aligned exactly 1 time 1662119 (9.19%) aligned >1 times 71.58% overall alignment rate Time searching: 00:05:07 Overall time: 00:05:07 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] 6046094 / 12946115 = 0.4670 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 10:42:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110314/SRX13110314.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110314/SRX13110314.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110314/SRX13110314.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110314/SRX13110314.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 10:42:57: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:42:57: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:43:04: 1000000 INFO @ Tue, 02 Aug 2022 10:43:10: 2000000 INFO @ Tue, 02 Aug 2022 10:43:16: 3000000 INFO @ Tue, 02 Aug 2022 10:43:22: 4000000 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 10:43:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110314/SRX13110314.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110314/SRX13110314.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110314/SRX13110314.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110314/SRX13110314.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 10:43:26: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:43:26: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:43:28: 5000000 INFO @ Tue, 02 Aug 2022 10:43:34: 1000000 INFO @ Tue, 02 Aug 2022 10:43:36: 6000000 INFO @ Tue, 02 Aug 2022 10:43:41: 2000000 INFO @ Tue, 02 Aug 2022 10:43:42: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:43:42: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:43:42: #1 total tags in treatment: 6900021 INFO @ Tue, 02 Aug 2022 10:43:42: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:43:42: #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 10:43:42: #1 tags after filtering in treatment: 6900021 INFO @ Tue, 02 Aug 2022 10:43:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:43:42: #1 finished! INFO @ Tue, 02 Aug 2022 10:43:42: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:43:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:43:42: #2 number of paired peaks: 1502 INFO @ Tue, 02 Aug 2022 10:43:42: start model_add_line... INFO @ Tue, 02 Aug 2022 10:43:43: start X-correlation... INFO @ Tue, 02 Aug 2022 10:43:43: end of X-cor INFO @ Tue, 02 Aug 2022 10:43:43: #2 finished! INFO @ Tue, 02 Aug 2022 10:43:43: #2 predicted fragment length is 187 bps INFO @ Tue, 02 Aug 2022 10:43:43: #2 alternative fragment length(s) may be 4,187 bps INFO @ Tue, 02 Aug 2022 10:43:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110314/SRX13110314.05_model.r INFO @ Tue, 02 Aug 2022 10:43:43: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:43:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:43:47: 3000000 INFO @ Tue, 02 Aug 2022 10:43:53: 4000000 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 10:43:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110314/SRX13110314.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110314/SRX13110314.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110314/SRX13110314.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110314/SRX13110314.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 10:43:56: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:43:56: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:44:00: 5000000 INFO @ Tue, 02 Aug 2022 10:44:00: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:44:04: 1000000 INFO @ Tue, 02 Aug 2022 10:44:07: 6000000 INFO @ Tue, 02 Aug 2022 10:44:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110314/SRX13110314.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:44:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110314/SRX13110314.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:44:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110314/SRX13110314.05_summits.bed INFO @ Tue, 02 Aug 2022 10:44:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2417 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:44:12: 2000000 INFO @ Tue, 02 Aug 2022 10:44:14: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:44:14: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:44:14: #1 total tags in treatment: 6900021 INFO @ Tue, 02 Aug 2022 10:44:14: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:44:14: #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 10:44:14: #1 tags after filtering in treatment: 6900021 INFO @ Tue, 02 Aug 2022 10:44:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:44:14: #1 finished! INFO @ Tue, 02 Aug 2022 10:44:14: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:44:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:44:14: #2 number of paired peaks: 1502 INFO @ Tue, 02 Aug 2022 10:44:14: start model_add_line... INFO @ Tue, 02 Aug 2022 10:44:14: start X-correlation... INFO @ Tue, 02 Aug 2022 10:44:14: end of X-cor INFO @ Tue, 02 Aug 2022 10:44:14: #2 finished! INFO @ Tue, 02 Aug 2022 10:44:14: #2 predicted fragment length is 187 bps INFO @ Tue, 02 Aug 2022 10:44:14: #2 alternative fragment length(s) may be 4,187 bps INFO @ Tue, 02 Aug 2022 10:44:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110314/SRX13110314.10_model.r INFO @ Tue, 02 Aug 2022 10:44:14: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:44:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:44:19: 3000000 INFO @ Tue, 02 Aug 2022 10:44:25: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:44:31: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:44:32: 5000000 INFO @ Tue, 02 Aug 2022 10:44:38: 6000000 INFO @ Tue, 02 Aug 2022 10:44:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110314/SRX13110314.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:44:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110314/SRX13110314.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:44:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110314/SRX13110314.10_summits.bed INFO @ Tue, 02 Aug 2022 10:44:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1221 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:44:43: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:44:43: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:44:43: #1 total tags in treatment: 6900021 INFO @ Tue, 02 Aug 2022 10:44:43: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:44:43: #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 10:44:43: #1 tags after filtering in treatment: 6900021 INFO @ Tue, 02 Aug 2022 10:44:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:44:43: #1 finished! INFO @ Tue, 02 Aug 2022 10:44:43: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:44:43: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:44:44: #2 number of paired peaks: 1502 INFO @ Tue, 02 Aug 2022 10:44:44: start model_add_line... INFO @ Tue, 02 Aug 2022 10:44:44: start X-correlation... INFO @ Tue, 02 Aug 2022 10:44:44: end of X-cor INFO @ Tue, 02 Aug 2022 10:44:44: #2 finished! INFO @ Tue, 02 Aug 2022 10:44:44: #2 predicted fragment length is 187 bps INFO @ Tue, 02 Aug 2022 10:44:44: #2 alternative fragment length(s) may be 4,187 bps INFO @ Tue, 02 Aug 2022 10:44:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110314/SRX13110314.20_model.r INFO @ Tue, 02 Aug 2022 10:44:44: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:44:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:45:02: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:45:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110314/SRX13110314.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:45:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110314/SRX13110314.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:45:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110314/SRX13110314.20_summits.bed INFO @ Tue, 02 Aug 2022 10:45:10: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (524 records, 4 fields): 10 millis CompletedMACS2peakCalling