Job ID = 6368591 SRX = SRX5020816 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:28:31 prefetch.2.10.7: 1) Downloading 'SRR8201439'... 2020-06-16T00:28:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:30:32 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:30:33 prefetch.2.10.7: 'SRR8201439' is valid 2020-06-16T00:30:33 prefetch.2.10.7: 1) 'SRR8201439' was downloaded successfully Read 14097384 spots for SRR8201439/SRR8201439.sra Written 14097384 spots for SRR8201439/SRR8201439.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: 00:03:26 14097384 reads; of these: 14097384 (100.00%) were unpaired; of these: 258664 (1.83%) aligned 0 times 11500677 (81.58%) aligned exactly 1 time 2338043 (16.58%) aligned >1 times 98.17% overall alignment rate Time searching: 00:03:26 Overall time: 00:03:26 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] 1083487 / 13838720 = 0.0783 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 09:38:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020816/SRX5020816.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020816/SRX5020816.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020816/SRX5020816.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020816/SRX5020816.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 09:38:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:38:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:39:01: 1000000 INFO @ Tue, 16 Jun 2020 09:39:07: 2000000 INFO @ Tue, 16 Jun 2020 09:39:14: 3000000 INFO @ Tue, 16 Jun 2020 09:39:20: 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 09:39:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020816/SRX5020816.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020816/SRX5020816.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020816/SRX5020816.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020816/SRX5020816.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 09:39:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:39:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:39:27: 5000000 INFO @ Tue, 16 Jun 2020 09:39:32: 1000000 INFO @ Tue, 16 Jun 2020 09:39:34: 6000000 INFO @ Tue, 16 Jun 2020 09:39:38: 2000000 INFO @ Tue, 16 Jun 2020 09:39:41: 7000000 INFO @ Tue, 16 Jun 2020 09:39:45: 3000000 INFO @ Tue, 16 Jun 2020 09:39:48: 8000000 INFO @ Tue, 16 Jun 2020 09:39:52: 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 09:39:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020816/SRX5020816.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020816/SRX5020816.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020816/SRX5020816.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020816/SRX5020816.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 09:39:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:39:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:39:55: 9000000 INFO @ Tue, 16 Jun 2020 09:39:59: 5000000 INFO @ Tue, 16 Jun 2020 09:40:02: 1000000 INFO @ Tue, 16 Jun 2020 09:40:02: 10000000 INFO @ Tue, 16 Jun 2020 09:40:06: 6000000 INFO @ Tue, 16 Jun 2020 09:40:09: 2000000 INFO @ Tue, 16 Jun 2020 09:40:09: 11000000 INFO @ Tue, 16 Jun 2020 09:40:13: 7000000 INFO @ Tue, 16 Jun 2020 09:40:16: 12000000 INFO @ Tue, 16 Jun 2020 09:40:16: 3000000 INFO @ Tue, 16 Jun 2020 09:40:20: 8000000 INFO @ Tue, 16 Jun 2020 09:40:21: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:40:21: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:40:21: #1 total tags in treatment: 12755233 INFO @ Tue, 16 Jun 2020 09:40:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:40:21: #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 09:40:21: #1 tags after filtering in treatment: 12755233 INFO @ Tue, 16 Jun 2020 09:40:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:40:21: #1 finished! INFO @ Tue, 16 Jun 2020 09:40:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:40:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:40:22: #2 number of paired peaks: 279 WARNING @ Tue, 16 Jun 2020 09:40:22: Fewer paired peaks (279) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 279 pairs to build model! INFO @ Tue, 16 Jun 2020 09:40:22: start model_add_line... INFO @ Tue, 16 Jun 2020 09:40:23: start X-correlation... INFO @ Tue, 16 Jun 2020 09:40:23: end of X-cor INFO @ Tue, 16 Jun 2020 09:40:23: #2 finished! INFO @ Tue, 16 Jun 2020 09:40:23: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:40:23: #2 alternative fragment length(s) may be 2,48 bps INFO @ Tue, 16 Jun 2020 09:40:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020816/SRX5020816.05_model.r WARNING @ Tue, 16 Jun 2020 09:40:23: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:40:23: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Tue, 16 Jun 2020 09:40:23: #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 09:40:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:40:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:40:23: 4000000 INFO @ Tue, 16 Jun 2020 09:40:27: 9000000 INFO @ Tue, 16 Jun 2020 09:40:30: 5000000 INFO @ Tue, 16 Jun 2020 09:40:34: 10000000 INFO @ Tue, 16 Jun 2020 09:40:37: 6000000 INFO @ Tue, 16 Jun 2020 09:40:41: 11000000 INFO @ Tue, 16 Jun 2020 09:40:44: 7000000 INFO @ Tue, 16 Jun 2020 09:40:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:40:48: 12000000 INFO @ Tue, 16 Jun 2020 09:40:51: 8000000 INFO @ Tue, 16 Jun 2020 09:40:53: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:40:53: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:40:53: #1 total tags in treatment: 12755233 INFO @ Tue, 16 Jun 2020 09:40:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:40:53: #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 09:40:54: #1 tags after filtering in treatment: 12755233 INFO @ Tue, 16 Jun 2020 09:40:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:40:54: #1 finished! INFO @ Tue, 16 Jun 2020 09:40:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:40:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:40:54: #2 number of paired peaks: 279 WARNING @ Tue, 16 Jun 2020 09:40:54: Fewer paired peaks (279) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 279 pairs to build model! INFO @ Tue, 16 Jun 2020 09:40:54: start model_add_line... INFO @ Tue, 16 Jun 2020 09:40:55: start X-correlation... INFO @ Tue, 16 Jun 2020 09:40:55: end of X-cor INFO @ Tue, 16 Jun 2020 09:40:55: #2 finished! INFO @ Tue, 16 Jun 2020 09:40:55: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:40:55: #2 alternative fragment length(s) may be 2,48 bps INFO @ Tue, 16 Jun 2020 09:40:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020816/SRX5020816.10_model.r WARNING @ Tue, 16 Jun 2020 09:40:55: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:40:55: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Tue, 16 Jun 2020 09:40:55: #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 09:40:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:40:55: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:40:57: 9000000 INFO @ Tue, 16 Jun 2020 09:41:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020816/SRX5020816.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:41:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020816/SRX5020816.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:41:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020816/SRX5020816.05_summits.bed INFO @ Tue, 16 Jun 2020 09:41:00: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (659 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:41:04: 10000000 INFO @ Tue, 16 Jun 2020 09:41:10: 11000000 INFO @ Tue, 16 Jun 2020 09:41:16: 12000000 INFO @ Tue, 16 Jun 2020 09:41:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:41:21: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:41:21: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:41:21: #1 total tags in treatment: 12755233 INFO @ Tue, 16 Jun 2020 09:41:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:41:21: #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 09:41:21: #1 tags after filtering in treatment: 12755233 INFO @ Tue, 16 Jun 2020 09:41:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:41:21: #1 finished! INFO @ Tue, 16 Jun 2020 09:41:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:41:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:41:22: #2 number of paired peaks: 279 WARNING @ Tue, 16 Jun 2020 09:41:22: Fewer paired peaks (279) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 279 pairs to build model! INFO @ Tue, 16 Jun 2020 09:41:22: start model_add_line... INFO @ Tue, 16 Jun 2020 09:41:22: start X-correlation... INFO @ Tue, 16 Jun 2020 09:41:22: end of X-cor INFO @ Tue, 16 Jun 2020 09:41:22: #2 finished! INFO @ Tue, 16 Jun 2020 09:41:22: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:41:22: #2 alternative fragment length(s) may be 2,48 bps INFO @ Tue, 16 Jun 2020 09:41:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020816/SRX5020816.20_model.r WARNING @ Tue, 16 Jun 2020 09:41:22: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:41:22: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Tue, 16 Jun 2020 09:41:22: #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 09:41:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:41:22: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:41:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020816/SRX5020816.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:41:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020816/SRX5020816.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:41:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020816/SRX5020816.10_summits.bed INFO @ Tue, 16 Jun 2020 09:41:32: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (444 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:41:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:41:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020816/SRX5020816.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:41:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020816/SRX5020816.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:41:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020816/SRX5020816.20_summits.bed INFO @ Tue, 16 Jun 2020 09:41:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (165 records, 4 fields): 1 millis CompletedMACS2peakCalling