Job ID = 16432311 SRX = SRX15407778 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T00:32:10 prefetch.2.10.7: 1) Downloading 'SRR19348973'... 2022-08-02T00:32:10 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T00:33:05 prefetch.2.10.7: HTTPS download succeed 2022-08-02T00:33:05 prefetch.2.10.7: 1) 'SRR19348973' was downloaded successfully 2022-08-02T00:33:05 prefetch.2.10.7: 'SRR19348973' has 0 unresolved dependencies Read 20407605 spots for SRR19348973/SRR19348973.sra Written 20407605 spots for SRR19348973/SRR19348973.sra fastq に変換しました。 bowtie でマッピング中... Your job 16433719 ("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: 00:05:47 20407605 reads; of these: 20407605 (100.00%) were unpaired; of these: 3168443 (15.53%) aligned 0 times 14780166 (72.42%) aligned exactly 1 time 2458996 (12.05%) aligned >1 times 84.47% overall alignment rate Time searching: 00:05:47 Overall time: 00:05:47 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] 2939272 / 17239162 = 0.1705 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 09:44:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX15407778/SRX15407778.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX15407778/SRX15407778.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX15407778/SRX15407778.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX15407778/SRX15407778.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 09:44:25: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:44:25: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:44:31: 1000000 INFO @ Tue, 02 Aug 2022 09:44:36: 2000000 INFO @ Tue, 02 Aug 2022 09:44:42: 3000000 INFO @ Tue, 02 Aug 2022 09:44:47: 4000000 INFO @ Tue, 02 Aug 2022 09:44:53: 5000000 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 09:44:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX15407778/SRX15407778.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX15407778/SRX15407778.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX15407778/SRX15407778.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX15407778/SRX15407778.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 09:44:55: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:44:55: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:44:59: 6000000 INFO @ Tue, 02 Aug 2022 09:45:01: 1000000 INFO @ Tue, 02 Aug 2022 09:45:05: 7000000 INFO @ Tue, 02 Aug 2022 09:45:07: 2000000 INFO @ Tue, 02 Aug 2022 09:45:11: 8000000 INFO @ Tue, 02 Aug 2022 09:45:13: 3000000 INFO @ Tue, 02 Aug 2022 09:45:17: 9000000 INFO @ Tue, 02 Aug 2022 09:45:19: 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 09:45:23: 10000000 INFO @ Tue, 02 Aug 2022 09:45:25: 5000000 INFO @ Tue, 02 Aug 2022 09:45:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX15407778/SRX15407778.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX15407778/SRX15407778.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX15407778/SRX15407778.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX15407778/SRX15407778.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 09:45:25: #1 read tag files... INFO @ Tue, 02 Aug 2022 09:45:25: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 09:45:30: 11000000 INFO @ Tue, 02 Aug 2022 09:45:32: 6000000 INFO @ Tue, 02 Aug 2022 09:45:32: 1000000 INFO @ Tue, 02 Aug 2022 09:45:36: 12000000 INFO @ Tue, 02 Aug 2022 09:45:38: 7000000 INFO @ Tue, 02 Aug 2022 09:45:39: 2000000 INFO @ Tue, 02 Aug 2022 09:45:42: 13000000 INFO @ Tue, 02 Aug 2022 09:45:44: 8000000 INFO @ Tue, 02 Aug 2022 09:45:46: 3000000 INFO @ Tue, 02 Aug 2022 09:45:49: 14000000 INFO @ Tue, 02 Aug 2022 09:45:50: 9000000 INFO @ Tue, 02 Aug 2022 09:45:51: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:45:51: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:45:51: #1 total tags in treatment: 14299890 INFO @ Tue, 02 Aug 2022 09:45:51: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:45:51: #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 09:45:51: #1 tags after filtering in treatment: 14299890 INFO @ Tue, 02 Aug 2022 09:45:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:45:51: #1 finished! INFO @ Tue, 02 Aug 2022 09:45:51: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:45:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:45:52: #2 number of paired peaks: 694 WARNING @ Tue, 02 Aug 2022 09:45:52: Fewer paired peaks (694) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 694 pairs to build model! INFO @ Tue, 02 Aug 2022 09:45:52: start model_add_line... INFO @ Tue, 02 Aug 2022 09:45:52: start X-correlation... INFO @ Tue, 02 Aug 2022 09:45:52: end of X-cor INFO @ Tue, 02 Aug 2022 09:45:52: #2 finished! INFO @ Tue, 02 Aug 2022 09:45:52: #2 predicted fragment length is 167 bps INFO @ Tue, 02 Aug 2022 09:45:52: #2 alternative fragment length(s) may be 167 bps INFO @ Tue, 02 Aug 2022 09:45:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX15407778/SRX15407778.05_model.r INFO @ Tue, 02 Aug 2022 09:45:52: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:45:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:45:53: 4000000 INFO @ Tue, 02 Aug 2022 09:45:56: 10000000 INFO @ Tue, 02 Aug 2022 09:46:00: 5000000 INFO @ Tue, 02 Aug 2022 09:46:03: 11000000 INFO @ Tue, 02 Aug 2022 09:46:07: 6000000 INFO @ Tue, 02 Aug 2022 09:46:09: 12000000 INFO @ Tue, 02 Aug 2022 09:46:14: 7000000 INFO @ Tue, 02 Aug 2022 09:46:15: 13000000 INFO @ Tue, 02 Aug 2022 09:46:21: 14000000 INFO @ Tue, 02 Aug 2022 09:46:21: 8000000 INFO @ Tue, 02 Aug 2022 09:46:22: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:46:23: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:46:23: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:46:23: #1 total tags in treatment: 14299890 INFO @ Tue, 02 Aug 2022 09:46:23: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:46:23: #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 09:46:23: #1 tags after filtering in treatment: 14299890 INFO @ Tue, 02 Aug 2022 09:46:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:46:23: #1 finished! INFO @ Tue, 02 Aug 2022 09:46:23: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:46:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:46:24: #2 number of paired peaks: 694 WARNING @ Tue, 02 Aug 2022 09:46:24: Fewer paired peaks (694) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 694 pairs to build model! INFO @ Tue, 02 Aug 2022 09:46:24: start model_add_line... INFO @ Tue, 02 Aug 2022 09:46:24: start X-correlation... INFO @ Tue, 02 Aug 2022 09:46:24: end of X-cor INFO @ Tue, 02 Aug 2022 09:46:24: #2 finished! INFO @ Tue, 02 Aug 2022 09:46:24: #2 predicted fragment length is 167 bps INFO @ Tue, 02 Aug 2022 09:46:24: #2 alternative fragment length(s) may be 167 bps INFO @ Tue, 02 Aug 2022 09:46:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX15407778/SRX15407778.10_model.r INFO @ Tue, 02 Aug 2022 09:46:24: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:46:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:46:27: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 09:46:34: 10000000 INFO @ Tue, 02 Aug 2022 09:46:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX15407778/SRX15407778.05_peaks.xls INFO @ Tue, 02 Aug 2022 09:46:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX15407778/SRX15407778.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:46:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX15407778/SRX15407778.05_summits.bed INFO @ Tue, 02 Aug 2022 09:46:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2492 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:46:40: 11000000 INFO @ Tue, 02 Aug 2022 09:46:47: 12000000 INFO @ Tue, 02 Aug 2022 09:46:53: 13000000 INFO @ Tue, 02 Aug 2022 09:46:54: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 09:46:59: 14000000 INFO @ Tue, 02 Aug 2022 09:47:01: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 09:47:01: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 09:47:01: #1 total tags in treatment: 14299890 INFO @ Tue, 02 Aug 2022 09:47:01: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 09:47:01: #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 09:47:01: #1 tags after filtering in treatment: 14299890 INFO @ Tue, 02 Aug 2022 09:47:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 09:47:01: #1 finished! INFO @ Tue, 02 Aug 2022 09:47:01: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 09:47:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 09:47:02: #2 number of paired peaks: 694 WARNING @ Tue, 02 Aug 2022 09:47:02: Fewer paired peaks (694) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 694 pairs to build model! INFO @ Tue, 02 Aug 2022 09:47:02: start model_add_line... INFO @ Tue, 02 Aug 2022 09:47:02: start X-correlation... INFO @ Tue, 02 Aug 2022 09:47:02: end of X-cor INFO @ Tue, 02 Aug 2022 09:47:02: #2 finished! INFO @ Tue, 02 Aug 2022 09:47:02: #2 predicted fragment length is 167 bps INFO @ Tue, 02 Aug 2022 09:47:02: #2 alternative fragment length(s) may be 167 bps INFO @ Tue, 02 Aug 2022 09:47:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX15407778/SRX15407778.20_model.r INFO @ Tue, 02 Aug 2022 09:47:02: #3 Call peaks... INFO @ Tue, 02 Aug 2022 09:47:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 09:47:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX15407778/SRX15407778.10_peaks.xls INFO @ Tue, 02 Aug 2022 09:47:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX15407778/SRX15407778.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:47:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX15407778/SRX15407778.10_summits.bed INFO @ Tue, 02 Aug 2022 09:47:08: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1618 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 09:47:32: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 09:47:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX15407778/SRX15407778.20_peaks.xls INFO @ Tue, 02 Aug 2022 09:47:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX15407778/SRX15407778.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 09:47:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX15407778/SRX15407778.20_summits.bed INFO @ Tue, 02 Aug 2022 09:47:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1030 records, 4 fields): 25 millis CompletedMACS2peakCalling