Job ID = 6366932 SRX = SRX2576634 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:59:53 prefetch.2.10.7: 1) Downloading 'SRR5272591'... 2020-06-15T22:59:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:01:00 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:01:01 prefetch.2.10.7: 'SRR5272591' is valid 2020-06-15T23:01:01 prefetch.2.10.7: 1) 'SRR5272591' was downloaded successfully Read 14369137 spots for SRR5272591/SRR5272591.sra Written 14369137 spots for SRR5272591/SRR5272591.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: 00:03:29 14369137 reads; of these: 14369137 (100.00%) were unpaired; of these: 593664 (4.13%) aligned 0 times 11397487 (79.32%) aligned exactly 1 time 2377986 (16.55%) aligned >1 times 95.87% overall alignment rate Time searching: 00:03:29 Overall time: 00:03:29 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] 4174171 / 13775473 = 0.3030 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 08:08:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576634/SRX2576634.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576634/SRX2576634.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576634/SRX2576634.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576634/SRX2576634.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 08:08:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:08:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:09:01: 1000000 INFO @ Tue, 16 Jun 2020 08:09:08: 2000000 INFO @ Tue, 16 Jun 2020 08:09:14: 3000000 INFO @ Tue, 16 Jun 2020 08:09:21: 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 08:09:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576634/SRX2576634.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576634/SRX2576634.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576634/SRX2576634.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576634/SRX2576634.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 08:09:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:09:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:09:27: 5000000 INFO @ Tue, 16 Jun 2020 08:09:31: 1000000 INFO @ Tue, 16 Jun 2020 08:09:34: 6000000 INFO @ Tue, 16 Jun 2020 08:09:38: 2000000 INFO @ Tue, 16 Jun 2020 08:09:41: 7000000 INFO @ Tue, 16 Jun 2020 08:09:44: 3000000 INFO @ Tue, 16 Jun 2020 08:09:48: 8000000 INFO @ Tue, 16 Jun 2020 08:09:50: 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 08:09:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576634/SRX2576634.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576634/SRX2576634.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576634/SRX2576634.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576634/SRX2576634.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 08:09:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:09:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:09:55: 9000000 INFO @ Tue, 16 Jun 2020 08:09:56: 5000000 INFO @ Tue, 16 Jun 2020 08:09:59: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:09:59: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:09:59: #1 total tags in treatment: 9601302 INFO @ Tue, 16 Jun 2020 08:09:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:09:59: #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 08:09:59: #1 tags after filtering in treatment: 9601302 INFO @ Tue, 16 Jun 2020 08:09:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:09:59: #1 finished! INFO @ Tue, 16 Jun 2020 08:09:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:09:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:10:00: #2 number of paired peaks: 369 WARNING @ Tue, 16 Jun 2020 08:10:00: Fewer paired peaks (369) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 369 pairs to build model! INFO @ Tue, 16 Jun 2020 08:10:00: start model_add_line... INFO @ Tue, 16 Jun 2020 08:10:00: start X-correlation... INFO @ Tue, 16 Jun 2020 08:10:00: end of X-cor INFO @ Tue, 16 Jun 2020 08:10:00: #2 finished! INFO @ Tue, 16 Jun 2020 08:10:00: #2 predicted fragment length is 46 bps INFO @ Tue, 16 Jun 2020 08:10:00: #2 alternative fragment length(s) may be 2,34,46 bps INFO @ Tue, 16 Jun 2020 08:10:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576634/SRX2576634.05_model.r WARNING @ Tue, 16 Jun 2020 08:10:00: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:10:00: #2 You may need to consider one of the other alternative d(s): 2,34,46 WARNING @ Tue, 16 Jun 2020 08:10:00: #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 08:10:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:10:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:10:01: 1000000 INFO @ Tue, 16 Jun 2020 08:10:02: 6000000 INFO @ Tue, 16 Jun 2020 08:10:08: 7000000 INFO @ Tue, 16 Jun 2020 08:10:08: 2000000 INFO @ Tue, 16 Jun 2020 08:10:14: 8000000 INFO @ Tue, 16 Jun 2020 08:10:15: 3000000 INFO @ Tue, 16 Jun 2020 08:10:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:10:20: 9000000 INFO @ Tue, 16 Jun 2020 08:10:22: 4000000 INFO @ Tue, 16 Jun 2020 08:10:24: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:10:24: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:10:24: #1 total tags in treatment: 9601302 INFO @ Tue, 16 Jun 2020 08:10:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:10:24: #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 08:10:24: #1 tags after filtering in treatment: 9601302 INFO @ Tue, 16 Jun 2020 08:10:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:10:24: #1 finished! INFO @ Tue, 16 Jun 2020 08:10:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:10:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:10:25: #2 number of paired peaks: 369 WARNING @ Tue, 16 Jun 2020 08:10:25: Fewer paired peaks (369) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 369 pairs to build model! INFO @ Tue, 16 Jun 2020 08:10:25: start model_add_line... INFO @ Tue, 16 Jun 2020 08:10:25: start X-correlation... INFO @ Tue, 16 Jun 2020 08:10:25: end of X-cor INFO @ Tue, 16 Jun 2020 08:10:25: #2 finished! INFO @ Tue, 16 Jun 2020 08:10:25: #2 predicted fragment length is 46 bps INFO @ Tue, 16 Jun 2020 08:10:25: #2 alternative fragment length(s) may be 2,34,46 bps INFO @ Tue, 16 Jun 2020 08:10:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576634/SRX2576634.10_model.r WARNING @ Tue, 16 Jun 2020 08:10:25: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:10:25: #2 You may need to consider one of the other alternative d(s): 2,34,46 WARNING @ Tue, 16 Jun 2020 08:10:25: #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 08:10:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:10:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:10:29: 5000000 INFO @ Tue, 16 Jun 2020 08:10:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576634/SRX2576634.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:10:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576634/SRX2576634.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:10:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576634/SRX2576634.05_summits.bed INFO @ Tue, 16 Jun 2020 08:10:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (693 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:10:35: 6000000 INFO @ Tue, 16 Jun 2020 08:10:42: 7000000 INFO @ Tue, 16 Jun 2020 08:10:44: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:10:48: 8000000 INFO @ Tue, 16 Jun 2020 08:10:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576634/SRX2576634.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:10:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576634/SRX2576634.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:10:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576634/SRX2576634.10_summits.bed INFO @ Tue, 16 Jun 2020 08:10:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (438 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:10:55: 9000000 INFO @ Tue, 16 Jun 2020 08:10:59: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:10:59: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:10:59: #1 total tags in treatment: 9601302 INFO @ Tue, 16 Jun 2020 08:10:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:10:59: #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 08:10:59: #1 tags after filtering in treatment: 9601302 INFO @ Tue, 16 Jun 2020 08:10:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:10:59: #1 finished! INFO @ Tue, 16 Jun 2020 08:10:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:10:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:11:00: #2 number of paired peaks: 369 WARNING @ Tue, 16 Jun 2020 08:11:00: Fewer paired peaks (369) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 369 pairs to build model! INFO @ Tue, 16 Jun 2020 08:11:00: start model_add_line... INFO @ Tue, 16 Jun 2020 08:11:00: start X-correlation... INFO @ Tue, 16 Jun 2020 08:11:00: end of X-cor INFO @ Tue, 16 Jun 2020 08:11:00: #2 finished! INFO @ Tue, 16 Jun 2020 08:11:00: #2 predicted fragment length is 46 bps INFO @ Tue, 16 Jun 2020 08:11:00: #2 alternative fragment length(s) may be 2,34,46 bps INFO @ Tue, 16 Jun 2020 08:11:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576634/SRX2576634.20_model.r WARNING @ Tue, 16 Jun 2020 08:11:00: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:11:00: #2 You may need to consider one of the other alternative d(s): 2,34,46 WARNING @ Tue, 16 Jun 2020 08:11:00: #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 08:11:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:11:00: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:11:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:11:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576634/SRX2576634.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:11:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576634/SRX2576634.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:11:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576634/SRX2576634.20_summits.bed INFO @ Tue, 16 Jun 2020 08:11:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (172 records, 4 fields): 1 millis CompletedMACS2peakCalling