Job ID = 10165626 SRX = SRX6799184 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 37933523 spots for SRR10065391/SRR10065391.sra Written 37933523 spots for SRR10065391/SRR10065391.sra fastq に変換しました。 bowtie でマッピング中... Your job 10165897 ("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: 00:08:16 37933523 reads; of these: 37933523 (100.00%) were unpaired; of these: 2476764 (6.53%) aligned 0 times 28320241 (74.66%) aligned exactly 1 time 7136518 (18.81%) aligned >1 times 93.47% overall alignment rate Time searching: 00:08:16 Overall time: 00:08:16 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 16 files... [bam_rmdupse_core] 10795830 / 35456759 = 0.3045 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 19:47:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.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 @ Thu, 08 Oct 2020 19:47:24: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:47:24: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:47:31: 1000000 INFO @ Thu, 08 Oct 2020 19:47:37: 2000000 INFO @ Thu, 08 Oct 2020 19:47:44: 3000000 INFO @ Thu, 08 Oct 2020 19:47:50: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 19:47:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.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 @ Thu, 08 Oct 2020 19:47:54: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:47:54: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:47:57: 5000000 INFO @ Thu, 08 Oct 2020 19:48:01: 1000000 INFO @ Thu, 08 Oct 2020 19:48:04: 6000000 INFO @ Thu, 08 Oct 2020 19:48:07: 2000000 INFO @ Thu, 08 Oct 2020 19:48:11: 7000000 INFO @ Thu, 08 Oct 2020 19:48:14: 3000000 INFO @ Thu, 08 Oct 2020 19:48:19: 8000000 INFO @ Thu, 08 Oct 2020 19:48:20: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 19:48:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.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 @ Thu, 08 Oct 2020 19:48:24: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:48:24: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:48:26: 9000000 INFO @ Thu, 08 Oct 2020 19:48:27: 5000000 INFO @ Thu, 08 Oct 2020 19:48:31: 1000000 INFO @ Thu, 08 Oct 2020 19:48:33: 10000000 INFO @ Thu, 08 Oct 2020 19:48:34: 6000000 INFO @ Thu, 08 Oct 2020 19:48:38: 2000000 INFO @ Thu, 08 Oct 2020 19:48:40: 11000000 INFO @ Thu, 08 Oct 2020 19:48:41: 7000000 INFO @ Thu, 08 Oct 2020 19:48:45: 3000000 INFO @ Thu, 08 Oct 2020 19:48:47: 12000000 INFO @ Thu, 08 Oct 2020 19:48:47: 8000000 INFO @ Thu, 08 Oct 2020 19:48:52: 4000000 INFO @ Thu, 08 Oct 2020 19:48:54: 9000000 INFO @ Thu, 08 Oct 2020 19:48:54: 13000000 INFO @ Thu, 08 Oct 2020 19:48:59: 5000000 INFO @ Thu, 08 Oct 2020 19:49:01: 10000000 INFO @ Thu, 08 Oct 2020 19:49:02: 14000000 INFO @ Thu, 08 Oct 2020 19:49:05: 6000000 INFO @ Thu, 08 Oct 2020 19:49:08: 11000000 INFO @ Thu, 08 Oct 2020 19:49:09: 15000000 INFO @ Thu, 08 Oct 2020 19:49:12: 7000000 INFO @ Thu, 08 Oct 2020 19:49:15: 12000000 INFO @ Thu, 08 Oct 2020 19:49:16: 16000000 INFO @ Thu, 08 Oct 2020 19:49:19: 8000000 INFO @ Thu, 08 Oct 2020 19:49:22: 13000000 INFO @ Thu, 08 Oct 2020 19:49:23: 17000000 INFO @ Thu, 08 Oct 2020 19:49:26: 9000000 INFO @ Thu, 08 Oct 2020 19:49:28: 14000000 INFO @ Thu, 08 Oct 2020 19:49:31: 18000000 INFO @ Thu, 08 Oct 2020 19:49:33: 10000000 INFO @ Thu, 08 Oct 2020 19:49:35: 15000000 INFO @ Thu, 08 Oct 2020 19:49:38: 19000000 INFO @ Thu, 08 Oct 2020 19:49:40: 11000000 INFO @ Thu, 08 Oct 2020 19:49:42: 16000000 INFO @ Thu, 08 Oct 2020 19:49:45: 20000000 INFO @ Thu, 08 Oct 2020 19:49:47: 12000000 INFO @ Thu, 08 Oct 2020 19:49:49: 17000000 INFO @ Thu, 08 Oct 2020 19:49:52: 21000000 INFO @ Thu, 08 Oct 2020 19:49:54: 13000000 INFO @ Thu, 08 Oct 2020 19:49:56: 18000000 INFO @ Thu, 08 Oct 2020 19:49:59: 22000000 INFO @ Thu, 08 Oct 2020 19:50:01: 14000000 INFO @ Thu, 08 Oct 2020 19:50:03: 19000000 INFO @ Thu, 08 Oct 2020 19:50:07: 23000000 INFO @ Thu, 08 Oct 2020 19:50:08: 15000000 INFO @ Thu, 08 Oct 2020 19:50:10: 20000000 INFO @ Thu, 08 Oct 2020 19:50:14: 24000000 INFO @ Thu, 08 Oct 2020 19:50:14: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 19:50:17: 21000000 INFO @ Thu, 08 Oct 2020 19:50:19: #1 tag size is determined as 49 bps INFO @ Thu, 08 Oct 2020 19:50:19: #1 tag size = 49 INFO @ Thu, 08 Oct 2020 19:50:19: #1 total tags in treatment: 24660929 INFO @ Thu, 08 Oct 2020 19:50:19: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:50:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 19:50:19: #1 tags after filtering in treatment: 24660929 INFO @ Thu, 08 Oct 2020 19:50:19: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:50:19: #1 finished! INFO @ Thu, 08 Oct 2020 19:50:19: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:50:19: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:50:21: #2 number of paired peaks: 224 WARNING @ Thu, 08 Oct 2020 19:50:21: Fewer paired peaks (224) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 224 pairs to build model! INFO @ Thu, 08 Oct 2020 19:50:21: start model_add_line... INFO @ Thu, 08 Oct 2020 19:50:21: start X-correlation... INFO @ Thu, 08 Oct 2020 19:50:21: end of X-cor INFO @ Thu, 08 Oct 2020 19:50:21: #2 finished! INFO @ Thu, 08 Oct 2020 19:50:21: #2 predicted fragment length is 295 bps INFO @ Thu, 08 Oct 2020 19:50:21: #2 alternative fragment length(s) may be 4,280,295 bps INFO @ Thu, 08 Oct 2020 19:50:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.05_model.r INFO @ Thu, 08 Oct 2020 19:50:21: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:50:21: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:50:21: 17000000 INFO @ Thu, 08 Oct 2020 19:50:23: 22000000 INFO @ Thu, 08 Oct 2020 19:50:28: 18000000 INFO @ Thu, 08 Oct 2020 19:50:30: 23000000 INFO @ Thu, 08 Oct 2020 19:50:35: 19000000 INFO @ Thu, 08 Oct 2020 19:50:36: 24000000 INFO @ Thu, 08 Oct 2020 19:50:40: #1 tag size is determined as 49 bps INFO @ Thu, 08 Oct 2020 19:50:40: #1 tag size = 49 INFO @ Thu, 08 Oct 2020 19:50:40: #1 total tags in treatment: 24660929 INFO @ Thu, 08 Oct 2020 19:50:40: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:50:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 19:50:41: #1 tags after filtering in treatment: 24660929 INFO @ Thu, 08 Oct 2020 19:50:41: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:50:41: #1 finished! INFO @ Thu, 08 Oct 2020 19:50:41: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:50:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:50:41: 20000000 INFO @ Thu, 08 Oct 2020 19:50:42: #2 number of paired peaks: 224 WARNING @ Thu, 08 Oct 2020 19:50:42: Fewer paired peaks (224) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 224 pairs to build model! INFO @ Thu, 08 Oct 2020 19:50:42: start model_add_line... INFO @ Thu, 08 Oct 2020 19:50:42: start X-correlation... INFO @ Thu, 08 Oct 2020 19:50:42: end of X-cor INFO @ Thu, 08 Oct 2020 19:50:42: #2 finished! INFO @ Thu, 08 Oct 2020 19:50:42: #2 predicted fragment length is 295 bps INFO @ Thu, 08 Oct 2020 19:50:42: #2 alternative fragment length(s) may be 4,280,295 bps INFO @ Thu, 08 Oct 2020 19:50:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.10_model.r INFO @ Thu, 08 Oct 2020 19:50:42: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:50:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:50:47: 21000000 INFO @ Thu, 08 Oct 2020 19:50:52: 22000000 INFO @ Thu, 08 Oct 2020 19:50:58: 23000000 BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 19:51:03: 24000000 INFO @ Thu, 08 Oct 2020 19:51:07: #1 tag size is determined as 49 bps INFO @ Thu, 08 Oct 2020 19:51:07: #1 tag size = 49 INFO @ Thu, 08 Oct 2020 19:51:07: #1 total tags in treatment: 24660929 INFO @ Thu, 08 Oct 2020 19:51:07: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:51:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 19:51:07: #1 tags after filtering in treatment: 24660929 INFO @ Thu, 08 Oct 2020 19:51:07: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:51:07: #1 finished! INFO @ Thu, 08 Oct 2020 19:51:07: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:51:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:51:09: #2 number of paired peaks: 224 WARNING @ Thu, 08 Oct 2020 19:51:09: Fewer paired peaks (224) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 224 pairs to build model! INFO @ Thu, 08 Oct 2020 19:51:09: start model_add_line... INFO @ Thu, 08 Oct 2020 19:51:09: start X-correlation... INFO @ Thu, 08 Oct 2020 19:51:09: end of X-cor INFO @ Thu, 08 Oct 2020 19:51:09: #2 finished! INFO @ Thu, 08 Oct 2020 19:51:09: #2 predicted fragment length is 295 bps INFO @ Thu, 08 Oct 2020 19:51:09: #2 alternative fragment length(s) may be 4,280,295 bps INFO @ Thu, 08 Oct 2020 19:51:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.20_model.r INFO @ Thu, 08 Oct 2020 19:51:09: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:51:09: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:51:21: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:51:43: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:51:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.05_peaks.xls INFO @ Thu, 08 Oct 2020 19:51:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:51:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.05_summits.bed INFO @ Thu, 08 Oct 2020 19:51:47: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (14706 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 19:52:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.10_peaks.xls INFO @ Thu, 08 Oct 2020 19:52:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:52:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.10_summits.bed INFO @ Thu, 08 Oct 2020 19:52:08: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (10906 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 19:52:10: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:52:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.20_peaks.xls INFO @ Thu, 08 Oct 2020 19:52:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:52:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799184/SRX6799184.20_summits.bed INFO @ Thu, 08 Oct 2020 19:52:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (6261 records, 4 fields): 7 millis CompletedMACS2peakCalling