Job ID = 16435412 SRX = SRX13110343 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T01:42:31 prefetch.2.10.7: 1) Downloading 'SRR16918013'... 2022-08-02T01:42:31 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T01:43:05 prefetch.2.10.7: HTTPS download succeed 2022-08-02T01:43:06 prefetch.2.10.7: 'SRR16918013' is valid 2022-08-02T01:43:06 prefetch.2.10.7: 1) 'SRR16918013' was downloaded successfully 2022-08-02T01:43:06 prefetch.2.10.7: 'SRR16918013' has 0 unresolved dependencies Read 16519686 spots for SRR16918013/SRR16918013.sra Written 16519686 spots for SRR16918013/SRR16918013.sra fastq に変換しました。 bowtie でマッピング中... Your job 16435591 ("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: 00:03:18 16519686 reads; of these: 16519686 (100.00%) were unpaired; of these: 8973868 (54.32%) aligned 0 times 6633657 (40.16%) aligned exactly 1 time 912161 (5.52%) aligned >1 times 45.68% overall alignment rate Time searching: 00:03:18 Overall time: 00:03:18 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] 1029886 / 7545818 = 0.1365 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 10:49:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110343/SRX13110343.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110343/SRX13110343.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110343/SRX13110343.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110343/SRX13110343.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 10:49:40: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:49:40: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:49:46: 1000000 INFO @ Tue, 02 Aug 2022 10:49:52: 2000000 INFO @ Tue, 02 Aug 2022 10:49:58: 3000000 INFO @ Tue, 02 Aug 2022 10:50:04: 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 10:50:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110343/SRX13110343.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110343/SRX13110343.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110343/SRX13110343.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110343/SRX13110343.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 10:50:09: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:50:09: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:50:09: 5000000 INFO @ Tue, 02 Aug 2022 10:50:16: 6000000 INFO @ Tue, 02 Aug 2022 10:50:16: 1000000 INFO @ Tue, 02 Aug 2022 10:50:19: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:50:19: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:50:19: #1 total tags in treatment: 6515932 INFO @ Tue, 02 Aug 2022 10:50:19: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:50:19: #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 10:50:19: #1 tags after filtering in treatment: 6515932 INFO @ Tue, 02 Aug 2022 10:50:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:50:19: #1 finished! INFO @ Tue, 02 Aug 2022 10:50:19: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:50:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:50:20: #2 number of paired peaks: 1070 INFO @ Tue, 02 Aug 2022 10:50:20: start model_add_line... INFO @ Tue, 02 Aug 2022 10:50:20: start X-correlation... INFO @ Tue, 02 Aug 2022 10:50:20: end of X-cor INFO @ Tue, 02 Aug 2022 10:50:20: #2 finished! INFO @ Tue, 02 Aug 2022 10:50:20: #2 predicted fragment length is 189 bps INFO @ Tue, 02 Aug 2022 10:50:20: #2 alternative fragment length(s) may be 189 bps INFO @ Tue, 02 Aug 2022 10:50:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110343/SRX13110343.05_model.r INFO @ Tue, 02 Aug 2022 10:50:20: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:50:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:50:23: 2000000 INFO @ Tue, 02 Aug 2022 10:50:29: 3000000 INFO @ Tue, 02 Aug 2022 10:50:34: 4000000 INFO @ Tue, 02 Aug 2022 10:50:35: #3 Call peaks for each chromosome... 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 10:50:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110343/SRX13110343.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110343/SRX13110343.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110343/SRX13110343.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110343/SRX13110343.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 10:50:39: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:50:39: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:50:40: 5000000 INFO @ Tue, 02 Aug 2022 10:50:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110343/SRX13110343.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:50:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110343/SRX13110343.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:50:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110343/SRX13110343.05_summits.bed INFO @ Tue, 02 Aug 2022 10:50:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5441 records, 4 fields): 102 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:50:46: 1000000 INFO @ Tue, 02 Aug 2022 10:50:46: 6000000 INFO @ Tue, 02 Aug 2022 10:50:50: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:50:50: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:50:50: #1 total tags in treatment: 6515932 INFO @ Tue, 02 Aug 2022 10:50:50: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:50:50: #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 10:50:50: #1 tags after filtering in treatment: 6515932 INFO @ Tue, 02 Aug 2022 10:50:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:50:50: #1 finished! INFO @ Tue, 02 Aug 2022 10:50:50: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:50:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:50:50: #2 number of paired peaks: 1070 INFO @ Tue, 02 Aug 2022 10:50:50: start model_add_line... INFO @ Tue, 02 Aug 2022 10:50:50: start X-correlation... INFO @ Tue, 02 Aug 2022 10:50:50: end of X-cor INFO @ Tue, 02 Aug 2022 10:50:50: #2 finished! INFO @ Tue, 02 Aug 2022 10:50:50: #2 predicted fragment length is 189 bps INFO @ Tue, 02 Aug 2022 10:50:50: #2 alternative fragment length(s) may be 189 bps INFO @ Tue, 02 Aug 2022 10:50:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110343/SRX13110343.10_model.r INFO @ Tue, 02 Aug 2022 10:50:50: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:50:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:50:52: 2000000 INFO @ Tue, 02 Aug 2022 10:50:58: 3000000 INFO @ Tue, 02 Aug 2022 10:51:04: 4000000 INFO @ Tue, 02 Aug 2022 10:51:05: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:51:10: 5000000 INFO @ Tue, 02 Aug 2022 10:51:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110343/SRX13110343.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:51:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110343/SRX13110343.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:51:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110343/SRX13110343.10_summits.bed INFO @ Tue, 02 Aug 2022 10:51:13: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3047 records, 4 fields): 55 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:51:16: 6000000 INFO @ Tue, 02 Aug 2022 10:51:18: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:51:18: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:51:18: #1 total tags in treatment: 6515932 INFO @ Tue, 02 Aug 2022 10:51:18: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:51:18: #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 10:51:18: #1 tags after filtering in treatment: 6515932 INFO @ Tue, 02 Aug 2022 10:51:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:51:18: #1 finished! INFO @ Tue, 02 Aug 2022 10:51:18: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:51:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:51:19: #2 number of paired peaks: 1070 INFO @ Tue, 02 Aug 2022 10:51:19: start model_add_line... INFO @ Tue, 02 Aug 2022 10:51:19: start X-correlation... INFO @ Tue, 02 Aug 2022 10:51:19: end of X-cor INFO @ Tue, 02 Aug 2022 10:51:19: #2 finished! INFO @ Tue, 02 Aug 2022 10:51:19: #2 predicted fragment length is 189 bps INFO @ Tue, 02 Aug 2022 10:51:19: #2 alternative fragment length(s) may be 189 bps INFO @ Tue, 02 Aug 2022 10:51:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110343/SRX13110343.20_model.r INFO @ Tue, 02 Aug 2022 10:51:19: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:51:19: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:51:34: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:51:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110343/SRX13110343.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:51:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110343/SRX13110343.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:51:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110343/SRX13110343.20_summits.bed INFO @ Tue, 02 Aug 2022 10:51:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1327 records, 4 fields): 117 millis CompletedMACS2peakCalling