Job ID = 10165634 SRX = SRX6799191 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 38761251 spots for SRR10065398/SRR10065398.sra Written 38761251 spots for SRR10065398/SRR10065398.sra fastq に変換しました。 bowtie でマッピング中... Your job 10165928 ("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: 00:09:30 38761251 reads; of these: 38761251 (100.00%) were unpaired; of these: 743842 (1.92%) aligned 0 times 27373172 (70.62%) aligned exactly 1 time 10644237 (27.46%) aligned >1 times 98.08% overall alignment rate Time searching: 00:09:30 Overall time: 00:09:30 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] 12071086 / 38017409 = 0.3175 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 19:49:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.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 19:49:52: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:49:52: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:49:58: 1000000 INFO @ Thu, 08 Oct 2020 19:50:04: 2000000 INFO @ Thu, 08 Oct 2020 19:50:10: 3000000 INFO @ Thu, 08 Oct 2020 19:50:15: 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 19:50:21: 5000000 INFO @ Thu, 08 Oct 2020 19:50:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.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 19:50:23: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:50:23: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:50:27: 6000000 INFO @ Thu, 08 Oct 2020 19:50:30: 1000000 INFO @ Thu, 08 Oct 2020 19:50:34: 7000000 INFO @ Thu, 08 Oct 2020 19:50:37: 2000000 INFO @ Thu, 08 Oct 2020 19:50:41: 8000000 INFO @ Thu, 08 Oct 2020 19:50:44: 3000000 INFO @ Thu, 08 Oct 2020 19:50:47: 9000000 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 19:50:51: 4000000 INFO @ Thu, 08 Oct 2020 19:50:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.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 19:50:52: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:50:52: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:50:54: 10000000 INFO @ Thu, 08 Oct 2020 19:50:58: 5000000 INFO @ Thu, 08 Oct 2020 19:51:00: 1000000 INFO @ Thu, 08 Oct 2020 19:51:00: 11000000 INFO @ Thu, 08 Oct 2020 19:51:06: 6000000 INFO @ Thu, 08 Oct 2020 19:51:07: 12000000 INFO @ Thu, 08 Oct 2020 19:51:07: 2000000 INFO @ Thu, 08 Oct 2020 19:51:13: 7000000 INFO @ Thu, 08 Oct 2020 19:51:14: 13000000 INFO @ Thu, 08 Oct 2020 19:51:15: 3000000 INFO @ Thu, 08 Oct 2020 19:51:20: 14000000 INFO @ Thu, 08 Oct 2020 19:51:21: 8000000 INFO @ Thu, 08 Oct 2020 19:51:23: 4000000 INFO @ Thu, 08 Oct 2020 19:51:27: 15000000 INFO @ Thu, 08 Oct 2020 19:51:29: 9000000 INFO @ Thu, 08 Oct 2020 19:51:30: 5000000 INFO @ Thu, 08 Oct 2020 19:51:34: 16000000 INFO @ Thu, 08 Oct 2020 19:51:36: 10000000 INFO @ Thu, 08 Oct 2020 19:51:38: 6000000 INFO @ Thu, 08 Oct 2020 19:51:40: 17000000 INFO @ Thu, 08 Oct 2020 19:51:44: 11000000 INFO @ Thu, 08 Oct 2020 19:51:46: 7000000 INFO @ Thu, 08 Oct 2020 19:51:47: 18000000 INFO @ Thu, 08 Oct 2020 19:51:52: 12000000 INFO @ Thu, 08 Oct 2020 19:51:53: 8000000 INFO @ Thu, 08 Oct 2020 19:51:54: 19000000 INFO @ Thu, 08 Oct 2020 19:51:59: 13000000 INFO @ Thu, 08 Oct 2020 19:52:01: 9000000 INFO @ Thu, 08 Oct 2020 19:52:01: 20000000 INFO @ Thu, 08 Oct 2020 19:52:07: 14000000 INFO @ Thu, 08 Oct 2020 19:52:08: 21000000 INFO @ Thu, 08 Oct 2020 19:52:09: 10000000 INFO @ Thu, 08 Oct 2020 19:52:14: 22000000 INFO @ Thu, 08 Oct 2020 19:52:15: 15000000 INFO @ Thu, 08 Oct 2020 19:52:16: 11000000 INFO @ Thu, 08 Oct 2020 19:52:21: 23000000 INFO @ Thu, 08 Oct 2020 19:52:22: 16000000 INFO @ Thu, 08 Oct 2020 19:52:23: 12000000 INFO @ Thu, 08 Oct 2020 19:52:28: 24000000 INFO @ Thu, 08 Oct 2020 19:52:31: 17000000 INFO @ Thu, 08 Oct 2020 19:52:31: 13000000 INFO @ Thu, 08 Oct 2020 19:52:35: 25000000 INFO @ Thu, 08 Oct 2020 19:52:38: 14000000 INFO @ Thu, 08 Oct 2020 19:52:39: 18000000 INFO @ Thu, 08 Oct 2020 19:52:41: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:52:41: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:52:41: #1 total tags in treatment: 25946323 INFO @ Thu, 08 Oct 2020 19:52:41: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:52:41: #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 19:52:41: #1 tags after filtering in treatment: 25946323 INFO @ Thu, 08 Oct 2020 19:52:41: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:52:41: #1 finished! INFO @ Thu, 08 Oct 2020 19:52:41: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:52:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:52:43: #2 number of paired peaks: 255 WARNING @ Thu, 08 Oct 2020 19:52:43: Fewer paired peaks (255) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 255 pairs to build model! INFO @ Thu, 08 Oct 2020 19:52:43: start model_add_line... INFO @ Thu, 08 Oct 2020 19:52:43: start X-correlation... INFO @ Thu, 08 Oct 2020 19:52:43: end of X-cor INFO @ Thu, 08 Oct 2020 19:52:43: #2 finished! INFO @ Thu, 08 Oct 2020 19:52:43: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 19:52:43: #2 alternative fragment length(s) may be 1,28,528,555,560,568 bps INFO @ Thu, 08 Oct 2020 19:52:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.05_model.r WARNING @ Thu, 08 Oct 2020 19:52:43: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:52:43: #2 You may need to consider one of the other alternative d(s): 1,28,528,555,560,568 WARNING @ Thu, 08 Oct 2020 19:52:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 19:52:43: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:52:43: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 19:52:45: 15000000 INFO @ Thu, 08 Oct 2020 19:52:47: 19000000 INFO @ Thu, 08 Oct 2020 19:52:52: 16000000 INFO @ Thu, 08 Oct 2020 19:52:54: 20000000 INFO @ Thu, 08 Oct 2020 19:53:00: 17000000 INFO @ Thu, 08 Oct 2020 19:53:01: 21000000 INFO @ Thu, 08 Oct 2020 19:53:07: 18000000 INFO @ Thu, 08 Oct 2020 19:53:08: 22000000 INFO @ Thu, 08 Oct 2020 19:53:14: 19000000 INFO @ Thu, 08 Oct 2020 19:53:15: 23000000 INFO @ Thu, 08 Oct 2020 19:53:20: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:53:21: 20000000 INFO @ Thu, 08 Oct 2020 19:53:22: 24000000 INFO @ Thu, 08 Oct 2020 19:53:28: 21000000 INFO @ Thu, 08 Oct 2020 19:53:29: 25000000 BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 19:53:35: 22000000 INFO @ Thu, 08 Oct 2020 19:53:36: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:53:36: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:53:36: #1 total tags in treatment: 25946323 INFO @ Thu, 08 Oct 2020 19:53:36: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:53:36: #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 19:53:36: #1 tags after filtering in treatment: 25946323 INFO @ Thu, 08 Oct 2020 19:53:36: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:53:36: #1 finished! INFO @ Thu, 08 Oct 2020 19:53:36: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:53:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:53:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.05_peaks.xls INFO @ Thu, 08 Oct 2020 19:53:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:53:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.05_summits.bed INFO @ Thu, 08 Oct 2020 19:53:37: Done! INFO @ Thu, 08 Oct 2020 19:53:38: #2 number of paired peaks: 255 WARNING @ Thu, 08 Oct 2020 19:53:38: Fewer paired peaks (255) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 255 pairs to build model! INFO @ Thu, 08 Oct 2020 19:53:38: start model_add_line... INFO @ Thu, 08 Oct 2020 19:53:38: start X-correlation... INFO @ Thu, 08 Oct 2020 19:53:38: end of X-cor INFO @ Thu, 08 Oct 2020 19:53:38: #2 finished! INFO @ Thu, 08 Oct 2020 19:53:38: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 19:53:38: #2 alternative fragment length(s) may be 1,28,528,555,560,568 bps INFO @ Thu, 08 Oct 2020 19:53:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.10_model.r WARNING @ Thu, 08 Oct 2020 19:53:38: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:53:38: #2 You may need to consider one of the other alternative d(s): 1,28,528,555,560,568 WARNING @ Thu, 08 Oct 2020 19:53:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 19:53:38: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:53:38: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 19:53:41: 23000000 INFO @ Thu, 08 Oct 2020 19:53:47: 24000000 INFO @ Thu, 08 Oct 2020 19:53:54: 25000000 INFO @ Thu, 08 Oct 2020 19:54:00: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:54:00: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:54:00: #1 total tags in treatment: 25946323 INFO @ Thu, 08 Oct 2020 19:54:00: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:54:00: #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 19:54:00: #1 tags after filtering in treatment: 25946323 INFO @ Thu, 08 Oct 2020 19:54:00: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:54:00: #1 finished! INFO @ Thu, 08 Oct 2020 19:54:00: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:54:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:54:02: #2 number of paired peaks: 255 WARNING @ Thu, 08 Oct 2020 19:54:02: Fewer paired peaks (255) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 255 pairs to build model! INFO @ Thu, 08 Oct 2020 19:54:02: start model_add_line... INFO @ Thu, 08 Oct 2020 19:54:02: start X-correlation... INFO @ Thu, 08 Oct 2020 19:54:02: end of X-cor INFO @ Thu, 08 Oct 2020 19:54:02: #2 finished! INFO @ Thu, 08 Oct 2020 19:54:02: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 19:54:02: #2 alternative fragment length(s) may be 1,28,528,555,560,568 bps INFO @ Thu, 08 Oct 2020 19:54:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.20_model.r WARNING @ Thu, 08 Oct 2020 19:54:02: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:54:02: #2 You may need to consider one of the other alternative d(s): 1,28,528,555,560,568 WARNING @ Thu, 08 Oct 2020 19:54:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 19:54:02: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:54:02: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:54:13: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:54:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.10_peaks.xls INFO @ Thu, 08 Oct 2020 19:54:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:54:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.10_summits.bed INFO @ Thu, 08 Oct 2020 19:54:29: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 19:54:36: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:54:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.20_peaks.xls INFO @ Thu, 08 Oct 2020 19:54:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:54:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799191/SRX6799191.20_summits.bed INFO @ Thu, 08 Oct 2020 19:54:52: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling