Job ID = 6368597 SRX = SRX5020822 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:24:48 prefetch.2.10.7: 1) Downloading 'SRR8201445'... 2020-06-16T00:24:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:26:34 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:26:35 prefetch.2.10.7: 'SRR8201445' is valid 2020-06-16T00:26:35 prefetch.2.10.7: 1) 'SRR8201445' was downloaded successfully Read 12038573 spots for SRR8201445/SRR8201445.sra Written 12038573 spots for SRR8201445/SRR8201445.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: 00:02:51 12038573 reads; of these: 12038573 (100.00%) were unpaired; of these: 161144 (1.34%) aligned 0 times 9943002 (82.59%) aligned exactly 1 time 1934427 (16.07%) aligned >1 times 98.66% overall alignment rate Time searching: 00:02:51 Overall time: 00:02:51 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 8 files... [bam_rmdupse_core] 887425 / 11877429 = 0.0747 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 09:33:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020822/SRX5020822.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020822/SRX5020822.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020822/SRX5020822.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020822/SRX5020822.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 09:33:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:33:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:33:45: 1000000 INFO @ Tue, 16 Jun 2020 09:33:52: 2000000 INFO @ Tue, 16 Jun 2020 09:33:59: 3000000 INFO @ Tue, 16 Jun 2020 09:34:05: 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 09:34:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020822/SRX5020822.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020822/SRX5020822.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020822/SRX5020822.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020822/SRX5020822.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 09:34:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:34:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:13: 5000000 INFO @ Tue, 16 Jun 2020 09:34:15: 1000000 INFO @ Tue, 16 Jun 2020 09:34:20: 6000000 INFO @ Tue, 16 Jun 2020 09:34:21: 2000000 INFO @ Tue, 16 Jun 2020 09:34:28: 7000000 INFO @ Tue, 16 Jun 2020 09:34:28: 3000000 INFO @ Tue, 16 Jun 2020 09:34:35: 4000000 INFO @ Tue, 16 Jun 2020 09:34:35: 8000000 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 09:34:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020822/SRX5020822.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020822/SRX5020822.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020822/SRX5020822.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020822/SRX5020822.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 09:34:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:34:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:41: 5000000 INFO @ Tue, 16 Jun 2020 09:34:43: 9000000 INFO @ Tue, 16 Jun 2020 09:34:45: 1000000 INFO @ Tue, 16 Jun 2020 09:34:48: 6000000 INFO @ Tue, 16 Jun 2020 09:34:50: 10000000 INFO @ Tue, 16 Jun 2020 09:34:51: 2000000 INFO @ Tue, 16 Jun 2020 09:34:55: 7000000 INFO @ Tue, 16 Jun 2020 09:34:58: 3000000 INFO @ Tue, 16 Jun 2020 09:34:58: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:34:58: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:34:58: #1 total tags in treatment: 10990004 INFO @ Tue, 16 Jun 2020 09:34:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:34:58: #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 09:34:58: #1 tags after filtering in treatment: 10990004 INFO @ Tue, 16 Jun 2020 09:34:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:34:58: #1 finished! INFO @ Tue, 16 Jun 2020 09:34:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:34:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:34:59: #2 number of paired peaks: 288 WARNING @ Tue, 16 Jun 2020 09:34:59: Fewer paired peaks (288) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 288 pairs to build model! INFO @ Tue, 16 Jun 2020 09:34:59: start model_add_line... INFO @ Tue, 16 Jun 2020 09:34:59: start X-correlation... INFO @ Tue, 16 Jun 2020 09:34:59: end of X-cor INFO @ Tue, 16 Jun 2020 09:34:59: #2 finished! INFO @ Tue, 16 Jun 2020 09:34:59: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:34:59: #2 alternative fragment length(s) may be 3,49 bps INFO @ Tue, 16 Jun 2020 09:34:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020822/SRX5020822.05_model.r WARNING @ Tue, 16 Jun 2020 09:34:59: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:34:59: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Tue, 16 Jun 2020 09:34:59: #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 09:34:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:34:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:35:01: 8000000 INFO @ Tue, 16 Jun 2020 09:35:05: 4000000 INFO @ Tue, 16 Jun 2020 09:35:08: 9000000 INFO @ Tue, 16 Jun 2020 09:35:11: 5000000 INFO @ Tue, 16 Jun 2020 09:35:15: 10000000 INFO @ Tue, 16 Jun 2020 09:35:18: 6000000 INFO @ Tue, 16 Jun 2020 09:35:21: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:35:21: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:35:21: #1 total tags in treatment: 10990004 INFO @ Tue, 16 Jun 2020 09:35:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:35:21: #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 09:35:21: #1 tags after filtering in treatment: 10990004 INFO @ Tue, 16 Jun 2020 09:35:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:35:21: #1 finished! INFO @ Tue, 16 Jun 2020 09:35:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:35:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:35:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:35:22: #2 number of paired peaks: 288 WARNING @ Tue, 16 Jun 2020 09:35:22: Fewer paired peaks (288) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 288 pairs to build model! INFO @ Tue, 16 Jun 2020 09:35:22: start model_add_line... INFO @ Tue, 16 Jun 2020 09:35:22: start X-correlation... INFO @ Tue, 16 Jun 2020 09:35:22: end of X-cor INFO @ Tue, 16 Jun 2020 09:35:22: #2 finished! INFO @ Tue, 16 Jun 2020 09:35:22: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:35:22: #2 alternative fragment length(s) may be 3,49 bps INFO @ Tue, 16 Jun 2020 09:35:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020822/SRX5020822.10_model.r WARNING @ Tue, 16 Jun 2020 09:35:22: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:35:22: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Tue, 16 Jun 2020 09:35:22: #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 09:35:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:35:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:35:24: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:35:30: 8000000 INFO @ Tue, 16 Jun 2020 09:35:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020822/SRX5020822.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:35:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020822/SRX5020822.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:35:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020822/SRX5020822.05_summits.bed INFO @ Tue, 16 Jun 2020 09:35:33: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (581 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:35:36: 9000000 INFO @ Tue, 16 Jun 2020 09:35:42: 10000000 INFO @ Tue, 16 Jun 2020 09:35:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:35:48: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:35:48: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:35:48: #1 total tags in treatment: 10990004 INFO @ Tue, 16 Jun 2020 09:35:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:35:48: #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 09:35:48: #1 tags after filtering in treatment: 10990004 INFO @ Tue, 16 Jun 2020 09:35:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:35:48: #1 finished! INFO @ Tue, 16 Jun 2020 09:35:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:35:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:35:49: #2 number of paired peaks: 288 WARNING @ Tue, 16 Jun 2020 09:35:49: Fewer paired peaks (288) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 288 pairs to build model! INFO @ Tue, 16 Jun 2020 09:35:49: start model_add_line... INFO @ Tue, 16 Jun 2020 09:35:49: start X-correlation... INFO @ Tue, 16 Jun 2020 09:35:49: end of X-cor INFO @ Tue, 16 Jun 2020 09:35:49: #2 finished! INFO @ Tue, 16 Jun 2020 09:35:49: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:35:49: #2 alternative fragment length(s) may be 3,49 bps INFO @ Tue, 16 Jun 2020 09:35:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020822/SRX5020822.20_model.r WARNING @ Tue, 16 Jun 2020 09:35:49: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:35:49: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Tue, 16 Jun 2020 09:35:49: #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 09:35:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:35:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:35:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020822/SRX5020822.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:35:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020822/SRX5020822.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:35:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020822/SRX5020822.10_summits.bed INFO @ Tue, 16 Jun 2020 09:35:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (390 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:36:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:36:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020822/SRX5020822.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:36:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020822/SRX5020822.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:36:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020822/SRX5020822.20_summits.bed INFO @ Tue, 16 Jun 2020 09:36:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (159 records, 4 fields): 2 millis CompletedMACS2peakCalling