Job ID = 6366882 SRX = SRX2543050 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:05:08 prefetch.2.10.7: 1) Downloading 'SRR5235986'... 2020-06-15T23:05:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:06:15 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:06:16 prefetch.2.10.7: 'SRR5235986' is valid 2020-06-15T23:06:16 prefetch.2.10.7: 1) 'SRR5235986' was downloaded successfully 2020-06-15T23:06:16 prefetch.2.10.7: 'SRR5235986' has 0 unresolved dependencies Read 18322182 spots for SRR5235986/SRR5235986.sra Written 18322182 spots for SRR5235986/SRR5235986.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: 00:06:16 18322182 reads; of these: 18322182 (100.00%) were unpaired; of these: 1429502 (7.80%) aligned 0 times 14120154 (77.07%) aligned exactly 1 time 2772526 (15.13%) aligned >1 times 92.20% overall alignment rate Time searching: 00:06:16 Overall time: 00:06:16 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] 2974316 / 16892680 = 0.1761 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 08:18:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2543050/SRX2543050.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2543050/SRX2543050.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2543050/SRX2543050.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2543050/SRX2543050.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 08:18:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:18:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:18:27: 1000000 INFO @ Tue, 16 Jun 2020 08:18:36: 2000000 INFO @ Tue, 16 Jun 2020 08:18:44: 3000000 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 08:18:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2543050/SRX2543050.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2543050/SRX2543050.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2543050/SRX2543050.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2543050/SRX2543050.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 08:18:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:18:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:18:53: 4000000 INFO @ Tue, 16 Jun 2020 08:18:59: 1000000 INFO @ Tue, 16 Jun 2020 08:19:02: 5000000 INFO @ Tue, 16 Jun 2020 08:19:08: 2000000 INFO @ Tue, 16 Jun 2020 08:19:12: 6000000 BedGraph に変換中... INFO @ Tue, 16 Jun 2020 08:19:17: 3000000 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 08:19:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2543050/SRX2543050.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2543050/SRX2543050.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2543050/SRX2543050.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2543050/SRX2543050.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 08:19:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:19:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:19:21: 7000000 INFO @ Tue, 16 Jun 2020 08:19:26: 4000000 INFO @ Tue, 16 Jun 2020 08:19:29: 1000000 INFO @ Tue, 16 Jun 2020 08:19:30: 8000000 INFO @ Tue, 16 Jun 2020 08:19:35: 5000000 INFO @ Tue, 16 Jun 2020 08:19:38: 2000000 INFO @ Tue, 16 Jun 2020 08:19:40: 9000000 INFO @ Tue, 16 Jun 2020 08:19:44: 6000000 INFO @ Tue, 16 Jun 2020 08:19:47: 3000000 INFO @ Tue, 16 Jun 2020 08:19:49: 10000000 INFO @ Tue, 16 Jun 2020 08:19:53: 7000000 INFO @ Tue, 16 Jun 2020 08:19:57: 4000000 INFO @ Tue, 16 Jun 2020 08:19:58: 11000000 INFO @ Tue, 16 Jun 2020 08:20:02: 8000000 INFO @ Tue, 16 Jun 2020 08:20:06: 5000000 INFO @ Tue, 16 Jun 2020 08:20:08: 12000000 INFO @ Tue, 16 Jun 2020 08:20:11: 9000000 INFO @ Tue, 16 Jun 2020 08:20:15: 6000000 INFO @ Tue, 16 Jun 2020 08:20:17: 13000000 INFO @ Tue, 16 Jun 2020 08:20:21: 10000000 INFO @ Tue, 16 Jun 2020 08:20:25: 7000000 INFO @ Tue, 16 Jun 2020 08:20:26: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:20:26: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:20:26: #1 total tags in treatment: 13918364 INFO @ Tue, 16 Jun 2020 08:20:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:20:26: #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 08:20:26: #1 tags after filtering in treatment: 13918364 INFO @ Tue, 16 Jun 2020 08:20:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:20:26: #1 finished! INFO @ Tue, 16 Jun 2020 08:20:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:20:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:20:27: #2 number of paired peaks: 240 WARNING @ Tue, 16 Jun 2020 08:20:27: Fewer paired peaks (240) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 240 pairs to build model! INFO @ Tue, 16 Jun 2020 08:20:27: start model_add_line... INFO @ Tue, 16 Jun 2020 08:20:27: start X-correlation... INFO @ Tue, 16 Jun 2020 08:20:27: end of X-cor INFO @ Tue, 16 Jun 2020 08:20:27: #2 finished! INFO @ Tue, 16 Jun 2020 08:20:27: #2 predicted fragment length is 62 bps INFO @ Tue, 16 Jun 2020 08:20:27: #2 alternative fragment length(s) may be 3,62 bps INFO @ Tue, 16 Jun 2020 08:20:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2543050/SRX2543050.05_model.r WARNING @ Tue, 16 Jun 2020 08:20:27: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:20:27: #2 You may need to consider one of the other alternative d(s): 3,62 WARNING @ Tue, 16 Jun 2020 08:20:27: #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 08:20:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:20:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:20:30: 11000000 INFO @ Tue, 16 Jun 2020 08:20:34: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:20:40: 12000000 INFO @ Tue, 16 Jun 2020 08:20:43: 9000000 INFO @ Tue, 16 Jun 2020 08:20:49: 13000000 INFO @ Tue, 16 Jun 2020 08:20:53: 10000000 INFO @ Tue, 16 Jun 2020 08:20:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:20:57: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:20:57: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:20:57: #1 total tags in treatment: 13918364 INFO @ Tue, 16 Jun 2020 08:20:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:20:57: #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 08:20:58: #1 tags after filtering in treatment: 13918364 INFO @ Tue, 16 Jun 2020 08:20:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:20:58: #1 finished! INFO @ Tue, 16 Jun 2020 08:20:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:20:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:20:59: #2 number of paired peaks: 240 WARNING @ Tue, 16 Jun 2020 08:20:59: Fewer paired peaks (240) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 240 pairs to build model! INFO @ Tue, 16 Jun 2020 08:20:59: start model_add_line... INFO @ Tue, 16 Jun 2020 08:20:59: start X-correlation... INFO @ Tue, 16 Jun 2020 08:20:59: end of X-cor INFO @ Tue, 16 Jun 2020 08:20:59: #2 finished! INFO @ Tue, 16 Jun 2020 08:20:59: #2 predicted fragment length is 62 bps INFO @ Tue, 16 Jun 2020 08:20:59: #2 alternative fragment length(s) may be 3,62 bps INFO @ Tue, 16 Jun 2020 08:20:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2543050/SRX2543050.10_model.r WARNING @ Tue, 16 Jun 2020 08:20:59: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:20:59: #2 You may need to consider one of the other alternative d(s): 3,62 WARNING @ Tue, 16 Jun 2020 08:20:59: #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 08:20:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:20:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:21:01: 11000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:21:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2543050/SRX2543050.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:21:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2543050/SRX2543050.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:21:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2543050/SRX2543050.05_summits.bed INFO @ Tue, 16 Jun 2020 08:21:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (966 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:21:10: 12000000 INFO @ Tue, 16 Jun 2020 08:21:18: 13000000 INFO @ Tue, 16 Jun 2020 08:21:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:21:25: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:21:25: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:21:25: #1 total tags in treatment: 13918364 INFO @ Tue, 16 Jun 2020 08:21:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:21:25: #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 08:21:26: #1 tags after filtering in treatment: 13918364 INFO @ Tue, 16 Jun 2020 08:21:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:21:26: #1 finished! INFO @ Tue, 16 Jun 2020 08:21:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:21:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:21:27: #2 number of paired peaks: 240 WARNING @ Tue, 16 Jun 2020 08:21:27: Fewer paired peaks (240) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 240 pairs to build model! INFO @ Tue, 16 Jun 2020 08:21:27: start model_add_line... INFO @ Tue, 16 Jun 2020 08:21:27: start X-correlation... INFO @ Tue, 16 Jun 2020 08:21:27: end of X-cor INFO @ Tue, 16 Jun 2020 08:21:27: #2 finished! INFO @ Tue, 16 Jun 2020 08:21:27: #2 predicted fragment length is 62 bps INFO @ Tue, 16 Jun 2020 08:21:27: #2 alternative fragment length(s) may be 3,62 bps INFO @ Tue, 16 Jun 2020 08:21:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2543050/SRX2543050.20_model.r WARNING @ Tue, 16 Jun 2020 08:21:27: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:21:27: #2 You may need to consider one of the other alternative d(s): 3,62 WARNING @ Tue, 16 Jun 2020 08:21:27: #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 08:21:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:21:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:21:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2543050/SRX2543050.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:21:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2543050/SRX2543050.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:21:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2543050/SRX2543050.10_summits.bed INFO @ Tue, 16 Jun 2020 08:21:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (420 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:21:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:22:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2543050/SRX2543050.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:22:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2543050/SRX2543050.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:22:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2543050/SRX2543050.20_summits.bed INFO @ Tue, 16 Jun 2020 08:22:05: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (189 records, 4 fields): 1 millis CompletedMACS2peakCalling