Job ID = 6368736 SRX = SRX5402760 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:27:19 prefetch.2.10.7: 1) Downloading 'SRR8602994'... 2020-06-16T00:27:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:30:41 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:30:41 prefetch.2.10.7: 1) 'SRR8602994' was downloaded successfully Read 26434432 spots for SRR8602994/SRR8602994.sra Written 26434432 spots for SRR8602994/SRR8602994.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: 00:05:56 26434432 reads; of these: 26434432 (100.00%) were unpaired; of these: 1351691 (5.11%) aligned 0 times 20746076 (78.48%) aligned exactly 1 time 4336665 (16.41%) aligned >1 times 94.89% overall alignment rate Time searching: 00:05:56 Overall time: 00:05:56 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] 6143648 / 25082741 = 0.2449 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 09:45:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402760/SRX5402760.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402760/SRX5402760.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402760/SRX5402760.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402760/SRX5402760.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 09:45:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:45:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:45:35: 1000000 INFO @ Tue, 16 Jun 2020 09:45:41: 2000000 INFO @ Tue, 16 Jun 2020 09:45:48: 3000000 INFO @ Tue, 16 Jun 2020 09:45:54: 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 09:45:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402760/SRX5402760.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402760/SRX5402760.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402760/SRX5402760.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402760/SRX5402760.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 09:45:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:45:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:46:01: 5000000 INFO @ Tue, 16 Jun 2020 09:46:03: 1000000 INFO @ Tue, 16 Jun 2020 09:46:07: 6000000 INFO @ Tue, 16 Jun 2020 09:46:08: 2000000 INFO @ Tue, 16 Jun 2020 09:46:13: 3000000 INFO @ Tue, 16 Jun 2020 09:46:14: 7000000 INFO @ Tue, 16 Jun 2020 09:46:18: 4000000 INFO @ Tue, 16 Jun 2020 09:46:20: 8000000 INFO @ Tue, 16 Jun 2020 09:46:23: 5000000 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 09:46:27: 9000000 INFO @ Tue, 16 Jun 2020 09:46:28: 6000000 INFO @ Tue, 16 Jun 2020 09:46:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402760/SRX5402760.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402760/SRX5402760.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402760/SRX5402760.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402760/SRX5402760.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 09:46:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:46:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:46:33: 7000000 INFO @ Tue, 16 Jun 2020 09:46:33: 10000000 INFO @ Tue, 16 Jun 2020 09:46:34: 1000000 INFO @ Tue, 16 Jun 2020 09:46:39: 8000000 INFO @ Tue, 16 Jun 2020 09:46:39: 2000000 INFO @ Tue, 16 Jun 2020 09:46:40: 11000000 INFO @ Tue, 16 Jun 2020 09:46:44: 9000000 INFO @ Tue, 16 Jun 2020 09:46:45: 3000000 INFO @ Tue, 16 Jun 2020 09:46:46: 12000000 INFO @ Tue, 16 Jun 2020 09:46:50: 10000000 INFO @ Tue, 16 Jun 2020 09:46:50: 4000000 INFO @ Tue, 16 Jun 2020 09:46:53: 13000000 INFO @ Tue, 16 Jun 2020 09:46:55: 11000000 INFO @ Tue, 16 Jun 2020 09:46:56: 5000000 INFO @ Tue, 16 Jun 2020 09:46:59: 14000000 INFO @ Tue, 16 Jun 2020 09:47:01: 12000000 INFO @ Tue, 16 Jun 2020 09:47:01: 6000000 INFO @ Tue, 16 Jun 2020 09:47:06: 15000000 INFO @ Tue, 16 Jun 2020 09:47:06: 13000000 INFO @ Tue, 16 Jun 2020 09:47:07: 7000000 INFO @ Tue, 16 Jun 2020 09:47:12: 14000000 INFO @ Tue, 16 Jun 2020 09:47:13: 16000000 INFO @ Tue, 16 Jun 2020 09:47:13: 8000000 INFO @ Tue, 16 Jun 2020 09:47:18: 15000000 INFO @ Tue, 16 Jun 2020 09:47:19: 9000000 INFO @ Tue, 16 Jun 2020 09:47:19: 17000000 INFO @ Tue, 16 Jun 2020 09:47:24: 16000000 INFO @ Tue, 16 Jun 2020 09:47:24: 10000000 INFO @ Tue, 16 Jun 2020 09:47:26: 18000000 INFO @ Tue, 16 Jun 2020 09:47:29: 17000000 INFO @ Tue, 16 Jun 2020 09:47:30: 11000000 INFO @ Tue, 16 Jun 2020 09:47:32: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:47:32: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:47:32: #1 total tags in treatment: 18939093 INFO @ Tue, 16 Jun 2020 09:47:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:47:32: #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 09:47:33: #1 tags after filtering in treatment: 18939093 INFO @ Tue, 16 Jun 2020 09:47:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:47:33: #1 finished! INFO @ Tue, 16 Jun 2020 09:47:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:47:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:47:34: #2 number of paired peaks: 296 WARNING @ Tue, 16 Jun 2020 09:47:34: Fewer paired peaks (296) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 296 pairs to build model! INFO @ Tue, 16 Jun 2020 09:47:34: start model_add_line... INFO @ Tue, 16 Jun 2020 09:47:34: start X-correlation... INFO @ Tue, 16 Jun 2020 09:47:34: end of X-cor INFO @ Tue, 16 Jun 2020 09:47:34: #2 finished! INFO @ Tue, 16 Jun 2020 09:47:34: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:47:34: #2 alternative fragment length(s) may be 1,37,551 bps INFO @ Tue, 16 Jun 2020 09:47:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402760/SRX5402760.05_model.r WARNING @ Tue, 16 Jun 2020 09:47:34: #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 09:47:34: #2 You may need to consider one of the other alternative d(s): 1,37,551 WARNING @ Tue, 16 Jun 2020 09:47:34: #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 09:47:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:47:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:47:35: 18000000 INFO @ Tue, 16 Jun 2020 09:47:36: 12000000 INFO @ Tue, 16 Jun 2020 09:47:40: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:47:40: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:47:40: #1 total tags in treatment: 18939093 INFO @ Tue, 16 Jun 2020 09:47:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:47:40: #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 09:47:41: #1 tags after filtering in treatment: 18939093 INFO @ Tue, 16 Jun 2020 09:47:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:47:41: #1 finished! INFO @ Tue, 16 Jun 2020 09:47:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:47:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:47:41: 13000000 INFO @ Tue, 16 Jun 2020 09:47:42: #2 number of paired peaks: 296 WARNING @ Tue, 16 Jun 2020 09:47:42: Fewer paired peaks (296) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 296 pairs to build model! INFO @ Tue, 16 Jun 2020 09:47:42: start model_add_line... INFO @ Tue, 16 Jun 2020 09:47:42: start X-correlation... INFO @ Tue, 16 Jun 2020 09:47:42: end of X-cor INFO @ Tue, 16 Jun 2020 09:47:42: #2 finished! INFO @ Tue, 16 Jun 2020 09:47:42: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:47:42: #2 alternative fragment length(s) may be 1,37,551 bps INFO @ Tue, 16 Jun 2020 09:47:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402760/SRX5402760.10_model.r WARNING @ Tue, 16 Jun 2020 09:47:42: #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 09:47:42: #2 You may need to consider one of the other alternative d(s): 1,37,551 WARNING @ Tue, 16 Jun 2020 09:47:42: #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 09:47:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:47:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:47:46: 14000000 INFO @ Tue, 16 Jun 2020 09:47:51: 15000000 INFO @ Tue, 16 Jun 2020 09:47:56: 16000000 INFO @ Tue, 16 Jun 2020 09:48:01: 17000000 INFO @ Tue, 16 Jun 2020 09:48:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:48:06: 18000000 INFO @ Tue, 16 Jun 2020 09:48:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:48:11: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:48:11: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:48:11: #1 total tags in treatment: 18939093 INFO @ Tue, 16 Jun 2020 09:48:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:48:11: #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 09:48:11: #1 tags after filtering in treatment: 18939093 INFO @ Tue, 16 Jun 2020 09:48:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:48:11: #1 finished! INFO @ Tue, 16 Jun 2020 09:48:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:48:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:48:12: #2 number of paired peaks: 296 WARNING @ Tue, 16 Jun 2020 09:48:12: Fewer paired peaks (296) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 296 pairs to build model! INFO @ Tue, 16 Jun 2020 09:48:12: start model_add_line... INFO @ Tue, 16 Jun 2020 09:48:12: start X-correlation... INFO @ Tue, 16 Jun 2020 09:48:12: end of X-cor INFO @ Tue, 16 Jun 2020 09:48:12: #2 finished! INFO @ Tue, 16 Jun 2020 09:48:12: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:48:12: #2 alternative fragment length(s) may be 1,37,551 bps INFO @ Tue, 16 Jun 2020 09:48:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402760/SRX5402760.20_model.r WARNING @ Tue, 16 Jun 2020 09:48:12: #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 09:48:12: #2 You may need to consider one of the other alternative d(s): 1,37,551 WARNING @ Tue, 16 Jun 2020 09:48:12: #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 09:48:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:48:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:48:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402760/SRX5402760.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:48:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402760/SRX5402760.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:48:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402760/SRX5402760.05_summits.bed INFO @ Tue, 16 Jun 2020 09:48:14: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:48:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402760/SRX5402760.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:48:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402760/SRX5402760.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:48:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402760/SRX5402760.10_summits.bed INFO @ Tue, 16 Jun 2020 09:48:23: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:48:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:48:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402760/SRX5402760.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:48:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402760/SRX5402760.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:48:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402760/SRX5402760.20_summits.bed INFO @ Tue, 16 Jun 2020 09:48:53: 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。