Job ID = 16433100 SRX = SRX10925644 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 22996189 spots for SRR14580034/SRR14580034.sra Written 22996189 spots for SRR14580034/SRR14580034.sra fastq に変換しました。 bowtie でマッピング中... Your job 16434328 ("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: 00:07:29 22996189 reads; of these: 22996189 (100.00%) were unpaired; of these: 7196302 (31.29%) aligned 0 times 11258716 (48.96%) aligned exactly 1 time 4541171 (19.75%) aligned >1 times 68.71% overall alignment rate Time searching: 00:07:29 Overall time: 00:07:29 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] 4558207 / 15799887 = 0.2885 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 09:51:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10925644/SRX10925644.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10925644/SRX10925644.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10925644/SRX10925644.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10925644/SRX10925644.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 09:51:27: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:51:27: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:51:37: 1000000 INFO @ Tue, 02 Aug 2022 09:51:47: 2000000 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 09:51:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10925644/SRX10925644.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10925644/SRX10925644.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10925644/SRX10925644.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10925644/SRX10925644.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 09:51:57: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:51:57: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:51:57: 3000000 INFO @ Tue, 02 Aug 2022 09:52:08: 4000000 INFO @ Tue, 02 Aug 2022 09:52:09: 1000000 INFO @ Tue, 02 Aug 2022 09:52:19: 5000000 INFO @ Tue, 02 Aug 2022 09:52:21: 2000000 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 09:52:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10925644/SRX10925644.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10925644/SRX10925644.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10925644/SRX10925644.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10925644/SRX10925644.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 09:52:27: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:52:27: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:52:30: 6000000 INFO @ Tue, 02 Aug 2022 09:52:33: 3000000 INFO @ Tue, 02 Aug 2022 09:52:39: 1000000 INFO @ Tue, 02 Aug 2022 09:52:41: 7000000 INFO @ Tue, 02 Aug 2022 09:52:46: 4000000 INFO @ Tue, 02 Aug 2022 09:52:52: 8000000 INFO @ Tue, 02 Aug 2022 09:52:52: 2000000 INFO @ Tue, 02 Aug 2022 09:52:58: 5000000 INFO @ Tue, 02 Aug 2022 09:53:03: 9000000 INFO @ Tue, 02 Aug 2022 09:53:04: 3000000 INFO @ Tue, 02 Aug 2022 09:53:10: 6000000 INFO @ Tue, 02 Aug 2022 09:53:14: 10000000 INFO @ Tue, 02 Aug 2022 09:53:16: 4000000 INFO @ Tue, 02 Aug 2022 09:53:22: 7000000 INFO @ Tue, 02 Aug 2022 09:53:24: 11000000 INFO @ Tue, 02 Aug 2022 09:53:27: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 09:53:27: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 09:53:27: #1 total tags in treatment: 11241680 INFO @ Tue, 02 Aug 2022 09:53:27: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:53:27: #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 09:53:27: #1 tags after filtering in treatment: 11241680 INFO @ Tue, 02 Aug 2022 09:53:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:53:27: #1 finished! INFO @ Tue, 02 Aug 2022 09:53:27: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:53:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:53:28: #2 number of paired peaks: 4057 INFO @ Tue, 02 Aug 2022 09:53:28: start model_add_line... INFO @ Tue, 02 Aug 2022 09:53:28: start X-correlation... INFO @ Tue, 02 Aug 2022 09:53:28: end of X-cor INFO @ Tue, 02 Aug 2022 09:53:28: #2 finished! INFO @ Tue, 02 Aug 2022 09:53:28: #2 predicted fragment length is 201 bps INFO @ Tue, 02 Aug 2022 09:53:28: #2 alternative fragment length(s) may be 201 bps INFO @ Tue, 02 Aug 2022 09:53:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10925644/SRX10925644.05_model.r INFO @ Tue, 02 Aug 2022 09:53:28: 5000000 INFO @ Tue, 02 Aug 2022 09:53:28: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:53:28: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 09:53:34: 8000000 INFO @ Tue, 02 Aug 2022 09:53:40: 6000000 INFO @ Tue, 02 Aug 2022 09:53:46: 9000000 INFO @ Tue, 02 Aug 2022 09:53:51: 7000000 INFO @ Tue, 02 Aug 2022 09:53:57: 10000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 09:54:03: 8000000 INFO @ Tue, 02 Aug 2022 09:54:03: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:54:08: 11000000 INFO @ Tue, 02 Aug 2022 09:54:11: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 09:54:11: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 09:54:11: #1 total tags in treatment: 11241680 INFO @ Tue, 02 Aug 2022 09:54:11: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:54:11: #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 09:54:11: #1 tags after filtering in treatment: 11241680 INFO @ Tue, 02 Aug 2022 09:54:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:54:11: #1 finished! INFO @ Tue, 02 Aug 2022 09:54:11: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:54:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:54:12: #2 number of paired peaks: 4057 INFO @ Tue, 02 Aug 2022 09:54:12: start model_add_line... INFO @ Tue, 02 Aug 2022 09:54:12: start X-correlation... INFO @ Tue, 02 Aug 2022 09:54:12: end of X-cor INFO @ Tue, 02 Aug 2022 09:54:12: #2 finished! INFO @ Tue, 02 Aug 2022 09:54:12: #2 predicted fragment length is 201 bps INFO @ Tue, 02 Aug 2022 09:54:12: #2 alternative fragment length(s) may be 201 bps INFO @ Tue, 02 Aug 2022 09:54:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10925644/SRX10925644.10_model.r INFO @ Tue, 02 Aug 2022 09:54:12: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:54:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:54:14: 9000000 INFO @ Tue, 02 Aug 2022 09:54:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10925644/SRX10925644.05_peaks.xls INFO @ Tue, 02 Aug 2022 09:54:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10925644/SRX10925644.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:54:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10925644/SRX10925644.05_summits.bed INFO @ Tue, 02 Aug 2022 09:54:17: Done! pass1 - making usageList (6 chroms): 4 millis pass2 - checking and writing primary data (22332 records, 4 fields): 46 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:54:24: 10000000 INFO @ Tue, 02 Aug 2022 09:54:33: 11000000 INFO @ Tue, 02 Aug 2022 09:54:35: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 09:54:35: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 09:54:35: #1 total tags in treatment: 11241680 INFO @ Tue, 02 Aug 2022 09:54:35: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:54:35: #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 09:54:35: #1 tags after filtering in treatment: 11241680 INFO @ Tue, 02 Aug 2022 09:54:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:54:35: #1 finished! INFO @ Tue, 02 Aug 2022 09:54:35: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:54:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:54:36: #2 number of paired peaks: 4057 INFO @ Tue, 02 Aug 2022 09:54:36: start model_add_line... INFO @ Tue, 02 Aug 2022 09:54:36: start X-correlation... INFO @ Tue, 02 Aug 2022 09:54:36: end of X-cor INFO @ Tue, 02 Aug 2022 09:54:36: #2 finished! INFO @ Tue, 02 Aug 2022 09:54:36: #2 predicted fragment length is 201 bps INFO @ Tue, 02 Aug 2022 09:54:36: #2 alternative fragment length(s) may be 201 bps INFO @ Tue, 02 Aug 2022 09:54:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10925644/SRX10925644.20_model.r INFO @ Tue, 02 Aug 2022 09:54:36: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:54:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:54:46: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:54:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10925644/SRX10925644.10_peaks.xls INFO @ Tue, 02 Aug 2022 09:54:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10925644/SRX10925644.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:54:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10925644/SRX10925644.10_summits.bed INFO @ Tue, 02 Aug 2022 09:54:59: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (15441 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:55:11: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:55:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10925644/SRX10925644.20_peaks.xls INFO @ Tue, 02 Aug 2022 09:55:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10925644/SRX10925644.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:55:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10925644/SRX10925644.20_summits.bed INFO @ Tue, 02 Aug 2022 09:55:23: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (7871 records, 4 fields): 37 millis CompletedMACS2peakCalling