Job ID = 10165630 SRX = SRX6799187 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 38150350 spots for SRR10065394/SRR10065394.sra Written 38150350 spots for SRR10065394/SRR10065394.sra fastq に変換しました。 bowtie でマッピング中... Your job 10165905 ("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: 00:08:26 38150350 reads; of these: 38150350 (100.00%) were unpaired; of these: 1481496 (3.88%) aligned 0 times 29053593 (76.16%) aligned exactly 1 time 7615261 (19.96%) aligned >1 times 96.12% overall alignment rate Time searching: 00:08:26 Overall time: 00:08:26 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] 11562172 / 36668854 = 0.3153 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 19:48:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799187/SRX6799187.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799187/SRX6799187.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799187/SRX6799187.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799187/SRX6799187.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 19:48:00: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:48:00: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:48:06: 1000000 INFO @ Thu, 08 Oct 2020 19:48:11: 2000000 INFO @ Thu, 08 Oct 2020 19:48:17: 3000000 INFO @ Thu, 08 Oct 2020 19:48:23: 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 19:48:29: 5000000 INFO @ Thu, 08 Oct 2020 19:48:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799187/SRX6799187.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799187/SRX6799187.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799187/SRX6799187.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799187/SRX6799187.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 19:48:29: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:48:29: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:48:35: 6000000 INFO @ Thu, 08 Oct 2020 19:48:36: 1000000 INFO @ Thu, 08 Oct 2020 19:48:41: 7000000 INFO @ Thu, 08 Oct 2020 19:48:42: 2000000 INFO @ Thu, 08 Oct 2020 19:48:47: 8000000 INFO @ Thu, 08 Oct 2020 19:48:48: 3000000 INFO @ Thu, 08 Oct 2020 19:48:54: 9000000 INFO @ Thu, 08 Oct 2020 19:48:54: 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 19:48:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799187/SRX6799187.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799187/SRX6799187.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799187/SRX6799187.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799187/SRX6799187.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 19:48:59: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:48:59: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:49:00: 10000000 INFO @ Thu, 08 Oct 2020 19:49:01: 5000000 INFO @ Thu, 08 Oct 2020 19:49:06: 1000000 INFO @ Thu, 08 Oct 2020 19:49:06: 11000000 INFO @ Thu, 08 Oct 2020 19:49:07: 6000000 INFO @ Thu, 08 Oct 2020 19:49:13: 2000000 INFO @ Thu, 08 Oct 2020 19:49:13: 12000000 INFO @ Thu, 08 Oct 2020 19:49:14: 7000000 INFO @ Thu, 08 Oct 2020 19:49:19: 13000000 INFO @ Thu, 08 Oct 2020 19:49:19: 3000000 INFO @ Thu, 08 Oct 2020 19:49:20: 8000000 INFO @ Thu, 08 Oct 2020 19:49:25: 14000000 INFO @ Thu, 08 Oct 2020 19:49:25: 4000000 INFO @ Thu, 08 Oct 2020 19:49:26: 9000000 INFO @ Thu, 08 Oct 2020 19:49:31: 15000000 INFO @ Thu, 08 Oct 2020 19:49:32: 5000000 INFO @ Thu, 08 Oct 2020 19:49:33: 10000000 INFO @ Thu, 08 Oct 2020 19:49:38: 16000000 INFO @ Thu, 08 Oct 2020 19:49:38: 6000000 INFO @ Thu, 08 Oct 2020 19:49:39: 11000000 INFO @ Thu, 08 Oct 2020 19:49:44: 17000000 INFO @ Thu, 08 Oct 2020 19:49:45: 7000000 INFO @ Thu, 08 Oct 2020 19:49:46: 12000000 INFO @ Thu, 08 Oct 2020 19:49:50: 18000000 INFO @ Thu, 08 Oct 2020 19:49:51: 8000000 INFO @ Thu, 08 Oct 2020 19:49:52: 13000000 INFO @ Thu, 08 Oct 2020 19:49:56: 19000000 INFO @ Thu, 08 Oct 2020 19:49:57: 9000000 INFO @ Thu, 08 Oct 2020 19:49:58: 14000000 INFO @ Thu, 08 Oct 2020 19:50:03: 20000000 INFO @ Thu, 08 Oct 2020 19:50:04: 10000000 INFO @ Thu, 08 Oct 2020 19:50:05: 15000000 INFO @ Thu, 08 Oct 2020 19:50:09: 21000000 INFO @ Thu, 08 Oct 2020 19:50:10: 11000000 INFO @ Thu, 08 Oct 2020 19:50:11: 16000000 INFO @ Thu, 08 Oct 2020 19:50:15: 22000000 INFO @ Thu, 08 Oct 2020 19:50:17: 17000000 INFO @ Thu, 08 Oct 2020 19:50:17: 12000000 INFO @ Thu, 08 Oct 2020 19:50:22: 23000000 INFO @ Thu, 08 Oct 2020 19:50:23: 18000000 INFO @ Thu, 08 Oct 2020 19:50:23: 13000000 INFO @ Thu, 08 Oct 2020 19:50:29: 24000000 INFO @ Thu, 08 Oct 2020 19:50:29: 19000000 INFO @ Thu, 08 Oct 2020 19:50:30: 14000000 INFO @ Thu, 08 Oct 2020 19:50:35: 25000000 INFO @ Thu, 08 Oct 2020 19:50:35: 20000000 INFO @ Thu, 08 Oct 2020 19:50:36: #1 tag size is determined as 49 bps INFO @ Thu, 08 Oct 2020 19:50:36: #1 tag size = 49 INFO @ Thu, 08 Oct 2020 19:50:36: #1 total tags in treatment: 25106682 INFO @ Thu, 08 Oct 2020 19:50:36: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:50:36: #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 19:50:36: #1 tags after filtering in treatment: 25106682 INFO @ Thu, 08 Oct 2020 19:50:36: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:50:36: #1 finished! INFO @ Thu, 08 Oct 2020 19:50:36: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:50:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:50:36: 15000000 INFO @ Thu, 08 Oct 2020 19:50:37: #2 number of paired peaks: 127 WARNING @ Thu, 08 Oct 2020 19:50:37: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Thu, 08 Oct 2020 19:50:37: start model_add_line... INFO @ Thu, 08 Oct 2020 19:50:38: start X-correlation... INFO @ Thu, 08 Oct 2020 19:50:38: end of X-cor INFO @ Thu, 08 Oct 2020 19:50:38: #2 finished! INFO @ Thu, 08 Oct 2020 19:50:38: #2 predicted fragment length is 138 bps INFO @ Thu, 08 Oct 2020 19:50:38: #2 alternative fragment length(s) may be 3,97,105,138 bps INFO @ Thu, 08 Oct 2020 19:50:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799187/SRX6799187.05_model.r INFO @ Thu, 08 Oct 2020 19:50:38: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:50:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:50:41: 21000000 INFO @ Thu, 08 Oct 2020 19:50:42: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 19:50:47: 22000000 INFO @ Thu, 08 Oct 2020 19:50:48: 17000000 INFO @ Thu, 08 Oct 2020 19:50:53: 23000000 INFO @ Thu, 08 Oct 2020 19:50:54: 18000000 INFO @ Thu, 08 Oct 2020 19:50:59: 24000000 INFO @ Thu, 08 Oct 2020 19:51:00: 19000000 INFO @ Thu, 08 Oct 2020 19:51:05: 25000000 INFO @ Thu, 08 Oct 2020 19:51:06: #1 tag size is determined as 49 bps INFO @ Thu, 08 Oct 2020 19:51:06: #1 tag size = 49 INFO @ Thu, 08 Oct 2020 19:51:06: #1 total tags in treatment: 25106682 INFO @ Thu, 08 Oct 2020 19:51:06: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:51:06: #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 19:51:06: #1 tags after filtering in treatment: 25106682 INFO @ Thu, 08 Oct 2020 19:51:06: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:51:06: #1 finished! INFO @ Thu, 08 Oct 2020 19:51:06: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:51:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:51:06: 20000000 INFO @ Thu, 08 Oct 2020 19:51:08: #2 number of paired peaks: 127 WARNING @ Thu, 08 Oct 2020 19:51:08: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Thu, 08 Oct 2020 19:51:08: start model_add_line... INFO @ Thu, 08 Oct 2020 19:51:08: start X-correlation... INFO @ Thu, 08 Oct 2020 19:51:08: end of X-cor INFO @ Thu, 08 Oct 2020 19:51:08: #2 finished! INFO @ Thu, 08 Oct 2020 19:51:08: #2 predicted fragment length is 138 bps INFO @ Thu, 08 Oct 2020 19:51:08: #2 alternative fragment length(s) may be 3,97,105,138 bps INFO @ Thu, 08 Oct 2020 19:51:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799187/SRX6799187.10_model.r INFO @ Thu, 08 Oct 2020 19:51:08: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:51:08: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:51:12: 21000000 INFO @ Thu, 08 Oct 2020 19:51:18: 22000000 INFO @ Thu, 08 Oct 2020 19:51:23: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:51:24: 23000000 BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 19:51:30: 24000000 INFO @ Thu, 08 Oct 2020 19:51:36: 25000000 INFO @ Thu, 08 Oct 2020 19:51:36: #1 tag size is determined as 49 bps INFO @ Thu, 08 Oct 2020 19:51:36: #1 tag size = 49 INFO @ Thu, 08 Oct 2020 19:51:36: #1 total tags in treatment: 25106682 INFO @ Thu, 08 Oct 2020 19:51:36: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:51:36: #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 19:51:37: #1 tags after filtering in treatment: 25106682 INFO @ Thu, 08 Oct 2020 19:51:37: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:51:37: #1 finished! INFO @ Thu, 08 Oct 2020 19:51:37: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:51:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:51:38: #2 number of paired peaks: 127 WARNING @ Thu, 08 Oct 2020 19:51:38: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Thu, 08 Oct 2020 19:51:38: start model_add_line... INFO @ Thu, 08 Oct 2020 19:51:38: start X-correlation... INFO @ Thu, 08 Oct 2020 19:51:38: end of X-cor INFO @ Thu, 08 Oct 2020 19:51:38: #2 finished! INFO @ Thu, 08 Oct 2020 19:51:38: #2 predicted fragment length is 138 bps INFO @ Thu, 08 Oct 2020 19:51:38: #2 alternative fragment length(s) may be 3,97,105,138 bps INFO @ Thu, 08 Oct 2020 19:51:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799187/SRX6799187.20_model.r INFO @ Thu, 08 Oct 2020 19:51:38: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:51:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:51:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799187/SRX6799187.05_peaks.xls INFO @ Thu, 08 Oct 2020 19:51:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799187/SRX6799187.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:51:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799187/SRX6799187.05_summits.bed INFO @ Thu, 08 Oct 2020 19:51:45: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (14455 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 19:51:53: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:52:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799187/SRX6799187.10_peaks.xls INFO @ Thu, 08 Oct 2020 19:52:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799187/SRX6799187.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:52:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799187/SRX6799187.10_summits.bed INFO @ Thu, 08 Oct 2020 19:52:14: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (9221 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 19:52:23: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:52:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799187/SRX6799187.20_peaks.xls INFO @ Thu, 08 Oct 2020 19:52:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799187/SRX6799187.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:52:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799187/SRX6799187.20_summits.bed INFO @ Thu, 08 Oct 2020 19:52:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3408 records, 4 fields): 5 millis CompletedMACS2peakCalling