Job ID = 6368670 SRX = SRX5402697 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:22:51 prefetch.2.10.7: 1) Downloading 'SRR8602931'... 2020-06-16T00:22:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:25:32 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:25:32 prefetch.2.10.7: 1) 'SRR8602931' was downloaded successfully Read 30711065 spots for SRR8602931/SRR8602931.sra Written 30711065 spots for SRR8602931/SRR8602931.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:32 30711065 reads; of these: 30711065 (100.00%) were unpaired; of these: 4697907 (15.30%) aligned 0 times 19260827 (62.72%) aligned exactly 1 time 6752331 (21.99%) aligned >1 times 84.70% overall alignment rate Time searching: 00:06:32 Overall time: 00:06:32 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 12 files... [bam_rmdupse_core] 6554335 / 26013158 = 0.2520 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 @ Tue, 16 Jun 2020 09:39:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402697/SRX5402697.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402697/SRX5402697.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402697/SRX5402697.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402697/SRX5402697.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, 16 Jun 2020 09:39:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:39:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:39:36: 1000000 INFO @ Tue, 16 Jun 2020 09:39:42: 2000000 INFO @ Tue, 16 Jun 2020 09:39:48: 3000000 INFO @ Tue, 16 Jun 2020 09:39:53: 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 @ Tue, 16 Jun 2020 09:39:59: 5000000 INFO @ Tue, 16 Jun 2020 09:40:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402697/SRX5402697.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402697/SRX5402697.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402697/SRX5402697.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402697/SRX5402697.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, 16 Jun 2020 09:40:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:40:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:40:05: 6000000 INFO @ Tue, 16 Jun 2020 09:40:06: 1000000 INFO @ Tue, 16 Jun 2020 09:40:11: 7000000 INFO @ Tue, 16 Jun 2020 09:40:12: 2000000 INFO @ Tue, 16 Jun 2020 09:40:17: 8000000 INFO @ Tue, 16 Jun 2020 09:40:18: 3000000 INFO @ Tue, 16 Jun 2020 09:40:23: 9000000 INFO @ Tue, 16 Jun 2020 09:40:24: 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 @ Tue, 16 Jun 2020 09:40:29: 10000000 INFO @ Tue, 16 Jun 2020 09:40:29: 5000000 INFO @ Tue, 16 Jun 2020 09:40:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402697/SRX5402697.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402697/SRX5402697.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402697/SRX5402697.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402697/SRX5402697.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, 16 Jun 2020 09:40:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:40:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:40:35: 11000000 INFO @ Tue, 16 Jun 2020 09:40:35: 6000000 INFO @ Tue, 16 Jun 2020 09:40:37: 1000000 INFO @ Tue, 16 Jun 2020 09:40:41: 12000000 INFO @ Tue, 16 Jun 2020 09:40:41: 7000000 INFO @ Tue, 16 Jun 2020 09:40:43: 2000000 INFO @ Tue, 16 Jun 2020 09:40:46: 8000000 INFO @ Tue, 16 Jun 2020 09:40:47: 13000000 INFO @ Tue, 16 Jun 2020 09:40:48: 3000000 INFO @ Tue, 16 Jun 2020 09:40:52: 9000000 INFO @ Tue, 16 Jun 2020 09:40:52: 14000000 INFO @ Tue, 16 Jun 2020 09:40:54: 4000000 INFO @ Tue, 16 Jun 2020 09:40:58: 10000000 INFO @ Tue, 16 Jun 2020 09:40:58: 15000000 INFO @ Tue, 16 Jun 2020 09:41:00: 5000000 INFO @ Tue, 16 Jun 2020 09:41:04: 11000000 INFO @ Tue, 16 Jun 2020 09:41:04: 16000000 INFO @ Tue, 16 Jun 2020 09:41:06: 6000000 INFO @ Tue, 16 Jun 2020 09:41:10: 12000000 INFO @ Tue, 16 Jun 2020 09:41:10: 17000000 INFO @ Tue, 16 Jun 2020 09:41:12: 7000000 INFO @ Tue, 16 Jun 2020 09:41:15: 13000000 INFO @ Tue, 16 Jun 2020 09:41:16: 18000000 INFO @ Tue, 16 Jun 2020 09:41:18: 8000000 INFO @ Tue, 16 Jun 2020 09:41:21: 14000000 INFO @ Tue, 16 Jun 2020 09:41:22: 19000000 INFO @ Tue, 16 Jun 2020 09:41:23: 9000000 INFO @ Tue, 16 Jun 2020 09:41:25: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:41:25: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:41:25: #1 total tags in treatment: 19458823 INFO @ Tue, 16 Jun 2020 09:41:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:41:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:41:25: #1 tags after filtering in treatment: 19458823 INFO @ Tue, 16 Jun 2020 09:41:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:41:25: #1 finished! INFO @ Tue, 16 Jun 2020 09:41:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:41:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:41:26: #2 number of paired peaks: 375 WARNING @ Tue, 16 Jun 2020 09:41:26: Fewer paired peaks (375) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 375 pairs to build model! INFO @ Tue, 16 Jun 2020 09:41:26: start model_add_line... INFO @ Tue, 16 Jun 2020 09:41:27: start X-correlation... INFO @ Tue, 16 Jun 2020 09:41:27: end of X-cor INFO @ Tue, 16 Jun 2020 09:41:27: #2 finished! INFO @ Tue, 16 Jun 2020 09:41:27: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:41:27: #2 alternative fragment length(s) may be 1,38,45,577,582 bps INFO @ Tue, 16 Jun 2020 09:41:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402697/SRX5402697.05_model.r WARNING @ Tue, 16 Jun 2020 09:41:27: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:41:27: #2 You may need to consider one of the other alternative d(s): 1,38,45,577,582 WARNING @ Tue, 16 Jun 2020 09:41:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:41:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:41:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:41:27: 15000000 INFO @ Tue, 16 Jun 2020 09:41:29: 10000000 INFO @ Tue, 16 Jun 2020 09:41:33: 16000000 INFO @ Tue, 16 Jun 2020 09:41:35: 11000000 INFO @ Tue, 16 Jun 2020 09:41:39: 17000000 INFO @ Tue, 16 Jun 2020 09:41:40: 12000000 INFO @ Tue, 16 Jun 2020 09:41:44: 18000000 INFO @ Tue, 16 Jun 2020 09:41:46: 13000000 INFO @ Tue, 16 Jun 2020 09:41:50: 19000000 INFO @ Tue, 16 Jun 2020 09:41:52: 14000000 INFO @ Tue, 16 Jun 2020 09:41:53: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:41:53: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:41:53: #1 total tags in treatment: 19458823 INFO @ Tue, 16 Jun 2020 09:41:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:41:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:41:53: #1 tags after filtering in treatment: 19458823 INFO @ Tue, 16 Jun 2020 09:41:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:41:53: #1 finished! INFO @ Tue, 16 Jun 2020 09:41:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:41:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:41:55: #2 number of paired peaks: 375 WARNING @ Tue, 16 Jun 2020 09:41:55: Fewer paired peaks (375) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 375 pairs to build model! INFO @ Tue, 16 Jun 2020 09:41:55: start model_add_line... INFO @ Tue, 16 Jun 2020 09:41:55: start X-correlation... INFO @ Tue, 16 Jun 2020 09:41:55: end of X-cor INFO @ Tue, 16 Jun 2020 09:41:55: #2 finished! INFO @ Tue, 16 Jun 2020 09:41:55: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:41:55: #2 alternative fragment length(s) may be 1,38,45,577,582 bps INFO @ Tue, 16 Jun 2020 09:41:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402697/SRX5402697.10_model.r WARNING @ Tue, 16 Jun 2020 09:41:55: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:41:55: #2 You may need to consider one of the other alternative d(s): 1,38,45,577,582 WARNING @ Tue, 16 Jun 2020 09:41:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:41:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:41:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:41:58: 15000000 INFO @ Tue, 16 Jun 2020 09:41:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:42:04: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:42:09: 17000000 INFO @ Tue, 16 Jun 2020 09:42:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402697/SRX5402697.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:42:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402697/SRX5402697.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:42:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402697/SRX5402697.05_summits.bed INFO @ Tue, 16 Jun 2020 09:42:14: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:42:15: 18000000 INFO @ Tue, 16 Jun 2020 09:42:21: 19000000 INFO @ Tue, 16 Jun 2020 09:42:23: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:42:23: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:42:23: #1 total tags in treatment: 19458823 INFO @ Tue, 16 Jun 2020 09:42:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:42:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:42:24: #1 tags after filtering in treatment: 19458823 INFO @ Tue, 16 Jun 2020 09:42:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:42:24: #1 finished! INFO @ Tue, 16 Jun 2020 09:42:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:42:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:42:25: #2 number of paired peaks: 375 WARNING @ Tue, 16 Jun 2020 09:42:25: Fewer paired peaks (375) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 375 pairs to build model! INFO @ Tue, 16 Jun 2020 09:42:25: start model_add_line... INFO @ Tue, 16 Jun 2020 09:42:25: start X-correlation... INFO @ Tue, 16 Jun 2020 09:42:25: end of X-cor INFO @ Tue, 16 Jun 2020 09:42:25: #2 finished! INFO @ Tue, 16 Jun 2020 09:42:25: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:42:25: #2 alternative fragment length(s) may be 1,38,45,577,582 bps INFO @ Tue, 16 Jun 2020 09:42:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402697/SRX5402697.20_model.r WARNING @ Tue, 16 Jun 2020 09:42:25: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:42:25: #2 You may need to consider one of the other alternative d(s): 1,38,45,577,582 WARNING @ Tue, 16 Jun 2020 09:42:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:42:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:42:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:42:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:42:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402697/SRX5402697.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:42:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402697/SRX5402697.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:42:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402697/SRX5402697.10_summits.bed INFO @ Tue, 16 Jun 2020 09:42:42: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:42:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:43:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402697/SRX5402697.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:43:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402697/SRX5402697.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:43:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402697/SRX5402697.20_summits.bed INFO @ Tue, 16 Jun 2020 09:43:12: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling