Job ID = 16435115 SRX = SRX13110328 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T01:34:47 prefetch.2.10.7: 1) Downloading 'SRR16917998'... 2022-08-02T01:34:47 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T01:35:24 prefetch.2.10.7: HTTPS download succeed 2022-08-02T01:35:25 prefetch.2.10.7: 'SRR16917998' is valid 2022-08-02T01:35:25 prefetch.2.10.7: 1) 'SRR16917998' was downloaded successfully 2022-08-02T01:35:25 prefetch.2.10.7: 'SRR16917998' has 0 unresolved dependencies Read 18467068 spots for SRR16917998/SRR16917998.sra Written 18467068 spots for SRR16917998/SRR16917998.sra fastq に変換しました。 bowtie でマッピング中... Your job 16435507 ("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: 00:03:02 18467068 reads; of these: 18467068 (100.00%) were unpaired; of these: 13338069 (72.23%) aligned 0 times 4442317 (24.06%) aligned exactly 1 time 686682 (3.72%) aligned >1 times 27.77% overall alignment rate Time searching: 00:03:02 Overall time: 00:03:02 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] 759411 / 5128999 = 0.1481 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 10:41:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110328/SRX13110328.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110328/SRX13110328.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110328/SRX13110328.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110328/SRX13110328.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 10:41:59: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:41:59: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:42:07: 1000000 INFO @ Tue, 02 Aug 2022 10:42:14: 2000000 INFO @ Tue, 02 Aug 2022 10:42:20: 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 10:42:27: 4000000 INFO @ Tue, 02 Aug 2022 10:42:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110328/SRX13110328.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110328/SRX13110328.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110328/SRX13110328.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110328/SRX13110328.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 10:42:29: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:42:29: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:42:30: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:42:30: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:42:30: #1 total tags in treatment: 4369588 INFO @ Tue, 02 Aug 2022 10:42:30: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:42:30: #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 10:42:30: #1 tags after filtering in treatment: 4369588 INFO @ Tue, 02 Aug 2022 10:42:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:42:30: #1 finished! INFO @ Tue, 02 Aug 2022 10:42:30: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:42:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:42:31: #2 number of paired peaks: 1454 INFO @ Tue, 02 Aug 2022 10:42:31: start model_add_line... INFO @ Tue, 02 Aug 2022 10:42:31: start X-correlation... INFO @ Tue, 02 Aug 2022 10:42:31: end of X-cor INFO @ Tue, 02 Aug 2022 10:42:31: #2 finished! INFO @ Tue, 02 Aug 2022 10:42:31: #2 predicted fragment length is 162 bps INFO @ Tue, 02 Aug 2022 10:42:31: #2 alternative fragment length(s) may be 162 bps INFO @ Tue, 02 Aug 2022 10:42:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110328/SRX13110328.05_model.r INFO @ Tue, 02 Aug 2022 10:42:31: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:42:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:42:35: 1000000 INFO @ Tue, 02 Aug 2022 10:42:41: 2000000 INFO @ Tue, 02 Aug 2022 10:42:42: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:42:47: 3000000 INFO @ Tue, 02 Aug 2022 10:42:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110328/SRX13110328.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:42:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110328/SRX13110328.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:42:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110328/SRX13110328.05_summits.bed INFO @ Tue, 02 Aug 2022 10:42:48: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2179 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:42:53: 4000000 INFO @ Tue, 02 Aug 2022 10:42:55: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:42:55: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:42:55: #1 total tags in treatment: 4369588 INFO @ Tue, 02 Aug 2022 10:42:55: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:42:55: #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 10:42:55: #1 tags after filtering in treatment: 4369588 INFO @ Tue, 02 Aug 2022 10:42:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:42:55: #1 finished! INFO @ Tue, 02 Aug 2022 10:42:55: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:42:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:42:55: #2 number of paired peaks: 1454 INFO @ Tue, 02 Aug 2022 10:42:55: start model_add_line... INFO @ Tue, 02 Aug 2022 10:42:55: start X-correlation... INFO @ Tue, 02 Aug 2022 10:42:55: end of X-cor INFO @ Tue, 02 Aug 2022 10:42:55: #2 finished! INFO @ Tue, 02 Aug 2022 10:42:55: #2 predicted fragment length is 162 bps INFO @ Tue, 02 Aug 2022 10:42:55: #2 alternative fragment length(s) may be 162 bps INFO @ Tue, 02 Aug 2022 10:42:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110328/SRX13110328.10_model.r INFO @ Tue, 02 Aug 2022 10:42:56: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:42:56: #3 Pre-compute pvalue-qvalue table... 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 10:42:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110328/SRX13110328.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110328/SRX13110328.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110328/SRX13110328.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110328/SRX13110328.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 10:42:59: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:42:59: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:43:06: 1000000 INFO @ Tue, 02 Aug 2022 10:43:06: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:43:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110328/SRX13110328.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:43:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110328/SRX13110328.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:43:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110328/SRX13110328.10_summits.bed INFO @ Tue, 02 Aug 2022 10:43:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1419 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:43:13: 2000000 INFO @ Tue, 02 Aug 2022 10:43:20: 3000000 INFO @ Tue, 02 Aug 2022 10:43:26: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:43:28: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:43:28: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:43:28: #1 total tags in treatment: 4369588 INFO @ Tue, 02 Aug 2022 10:43:28: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:43:28: #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 10:43:28: #1 tags after filtering in treatment: 4369588 INFO @ Tue, 02 Aug 2022 10:43:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:43:28: #1 finished! INFO @ Tue, 02 Aug 2022 10:43:28: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:43:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:43:29: #2 number of paired peaks: 1454 INFO @ Tue, 02 Aug 2022 10:43:29: start model_add_line... INFO @ Tue, 02 Aug 2022 10:43:29: start X-correlation... INFO @ Tue, 02 Aug 2022 10:43:29: end of X-cor INFO @ Tue, 02 Aug 2022 10:43:29: #2 finished! INFO @ Tue, 02 Aug 2022 10:43:29: #2 predicted fragment length is 162 bps INFO @ Tue, 02 Aug 2022 10:43:29: #2 alternative fragment length(s) may be 162 bps INFO @ Tue, 02 Aug 2022 10:43:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110328/SRX13110328.20_model.r INFO @ Tue, 02 Aug 2022 10:43:29: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:43:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:43:40: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:43:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110328/SRX13110328.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:43:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110328/SRX13110328.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:43:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110328/SRX13110328.20_summits.bed INFO @ Tue, 02 Aug 2022 10:43:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (890 records, 4 fields): 367 millis CompletedMACS2peakCalling