Job ID = 6368575 SRX = SRX5020801 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:25:46 prefetch.2.10.7: 1) Downloading 'SRR8201424'... 2020-06-16T00:25:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:26:45 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:26:46 prefetch.2.10.7: 'SRR8201424' is valid 2020-06-16T00:26:46 prefetch.2.10.7: 1) 'SRR8201424' was downloaded successfully 2020-06-16T00:26:46 prefetch.2.10.7: 'SRR8201424' has 0 unresolved dependencies Read 6103851 spots for SRR8201424/SRR8201424.sra Written 6103851 spots for SRR8201424/SRR8201424.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: 00:00:01 Multiseed full-index search: 00:02:07 6103851 reads; of these: 6103851 (100.00%) were unpaired; of these: 337672 (5.53%) aligned 0 times 4826346 (79.07%) aligned exactly 1 time 939833 (15.40%) aligned >1 times 94.47% overall alignment rate Time searching: 00:02:08 Overall time: 00:02:08 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_rmdupse_core] 276871 / 5766179 = 0.0480 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 09:31:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020801/SRX5020801.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020801/SRX5020801.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020801/SRX5020801.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020801/SRX5020801.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 09:31:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:31:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:31:48: 1000000 INFO @ Tue, 16 Jun 2020 09:31:54: 2000000 INFO @ Tue, 16 Jun 2020 09:32:01: 3000000 INFO @ Tue, 16 Jun 2020 09:32:07: 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 09:32:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020801/SRX5020801.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020801/SRX5020801.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020801/SRX5020801.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020801/SRX5020801.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 09:32:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:32:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:32:14: 5000000 INFO @ Tue, 16 Jun 2020 09:32:18: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:32:18: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:32:18: #1 total tags in treatment: 5489308 INFO @ Tue, 16 Jun 2020 09:32:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:32:18: #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 09:32:18: #1 tags after filtering in treatment: 5489308 INFO @ Tue, 16 Jun 2020 09:32:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:32:18: #1 finished! INFO @ Tue, 16 Jun 2020 09:32:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:32:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:32:18: #2 number of paired peaks: 360 WARNING @ Tue, 16 Jun 2020 09:32:18: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Tue, 16 Jun 2020 09:32:18: start model_add_line... INFO @ Tue, 16 Jun 2020 09:32:18: start X-correlation... INFO @ Tue, 16 Jun 2020 09:32:18: end of X-cor INFO @ Tue, 16 Jun 2020 09:32:18: #2 finished! INFO @ Tue, 16 Jun 2020 09:32:18: #2 predicted fragment length is 75 bps INFO @ Tue, 16 Jun 2020 09:32:18: #2 alternative fragment length(s) may be 75 bps INFO @ Tue, 16 Jun 2020 09:32:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020801/SRX5020801.05_model.r WARNING @ Tue, 16 Jun 2020 09:32:18: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:32:18: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Tue, 16 Jun 2020 09:32:18: #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 09:32:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:32:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:32:19: 1000000 INFO @ Tue, 16 Jun 2020 09:32:27: 2000000 INFO @ Tue, 16 Jun 2020 09:32:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:32:34: 3000000 INFO @ Tue, 16 Jun 2020 09:32:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020801/SRX5020801.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:32:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020801/SRX5020801.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:32:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020801/SRX5020801.05_summits.bed INFO @ Tue, 16 Jun 2020 09:32:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (454 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 09:32:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020801/SRX5020801.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020801/SRX5020801.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020801/SRX5020801.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020801/SRX5020801.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 09:32:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:32:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:32:42: 4000000 INFO @ Tue, 16 Jun 2020 09:32:49: 1000000 INFO @ Tue, 16 Jun 2020 09:32:50: 5000000 INFO @ Tue, 16 Jun 2020 09:32:54: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:32:54: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:32:54: #1 total tags in treatment: 5489308 INFO @ Tue, 16 Jun 2020 09:32:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:32:54: #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 09:32:54: #1 tags after filtering in treatment: 5489308 INFO @ Tue, 16 Jun 2020 09:32:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:32:54: #1 finished! INFO @ Tue, 16 Jun 2020 09:32:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:32:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:32:55: #2 number of paired peaks: 360 WARNING @ Tue, 16 Jun 2020 09:32:55: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Tue, 16 Jun 2020 09:32:55: start model_add_line... INFO @ Tue, 16 Jun 2020 09:32:55: start X-correlation... INFO @ Tue, 16 Jun 2020 09:32:55: end of X-cor INFO @ Tue, 16 Jun 2020 09:32:55: #2 finished! INFO @ Tue, 16 Jun 2020 09:32:55: #2 predicted fragment length is 75 bps INFO @ Tue, 16 Jun 2020 09:32:55: #2 alternative fragment length(s) may be 75 bps INFO @ Tue, 16 Jun 2020 09:32:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020801/SRX5020801.10_model.r WARNING @ Tue, 16 Jun 2020 09:32:55: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:32:55: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Tue, 16 Jun 2020 09:32:55: #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 09:32:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:32:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:32:56: 2000000 INFO @ Tue, 16 Jun 2020 09:33:03: 3000000 INFO @ Tue, 16 Jun 2020 09:33:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:33:10: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:33:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020801/SRX5020801.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:33:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020801/SRX5020801.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:33:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020801/SRX5020801.10_summits.bed INFO @ Tue, 16 Jun 2020 09:33:13: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (312 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:33:17: 5000000 INFO @ Tue, 16 Jun 2020 09:33:20: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:33:20: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:33:20: #1 total tags in treatment: 5489308 INFO @ Tue, 16 Jun 2020 09:33:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:33:20: #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 09:33:21: #1 tags after filtering in treatment: 5489308 INFO @ Tue, 16 Jun 2020 09:33:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:33:21: #1 finished! INFO @ Tue, 16 Jun 2020 09:33:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:33:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:33:21: #2 number of paired peaks: 360 WARNING @ Tue, 16 Jun 2020 09:33:21: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Tue, 16 Jun 2020 09:33:21: start model_add_line... INFO @ Tue, 16 Jun 2020 09:33:21: start X-correlation... INFO @ Tue, 16 Jun 2020 09:33:21: end of X-cor INFO @ Tue, 16 Jun 2020 09:33:21: #2 finished! INFO @ Tue, 16 Jun 2020 09:33:21: #2 predicted fragment length is 75 bps INFO @ Tue, 16 Jun 2020 09:33:21: #2 alternative fragment length(s) may be 75 bps INFO @ Tue, 16 Jun 2020 09:33:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020801/SRX5020801.20_model.r WARNING @ Tue, 16 Jun 2020 09:33:21: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:33:21: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Tue, 16 Jun 2020 09:33:21: #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 09:33:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:33:21: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:33:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:33:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020801/SRX5020801.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:33:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020801/SRX5020801.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:33:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020801/SRX5020801.20_summits.bed INFO @ Tue, 16 Jun 2020 09:33:39: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (175 records, 4 fields): 1 millis CompletedMACS2peakCalling