Job ID = 6366751 SRX = SRX2228904 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:54:44 prefetch.2.10.7: 1) Downloading 'SRR4380360'... 2020-06-15T22:54:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:55:53 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:55:54 prefetch.2.10.7: 'SRR4380360' is valid 2020-06-15T22:55:54 prefetch.2.10.7: 1) 'SRR4380360' was downloaded successfully 2020-06-15T22:55:54 prefetch.2.10.7: 'SRR4380360' has 0 unresolved dependencies Read 16861980 spots for SRR4380360/SRR4380360.sra Written 16861980 spots for SRR4380360/SRR4380360.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: 00:04:00 16861980 reads; of these: 16861980 (100.00%) were unpaired; of these: 165759 (0.98%) aligned 0 times 13890788 (82.38%) aligned exactly 1 time 2805433 (16.64%) aligned >1 times 99.02% overall alignment rate Time searching: 00:04:00 Overall time: 00:04:00 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] 1495640 / 16696221 = 0.0896 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 08:05:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228904/SRX2228904.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228904/SRX2228904.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228904/SRX2228904.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228904/SRX2228904.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 08:05:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:05:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:05:24: 1000000 INFO @ Tue, 16 Jun 2020 08:05:29: 2000000 INFO @ Tue, 16 Jun 2020 08:05:34: 3000000 INFO @ Tue, 16 Jun 2020 08:05:40: 4000000 INFO @ Tue, 16 Jun 2020 08:05:45: 5000000 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 08:05:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228904/SRX2228904.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228904/SRX2228904.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228904/SRX2228904.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228904/SRX2228904.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 08:05:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:05:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:05:50: 6000000 INFO @ Tue, 16 Jun 2020 08:05:54: 1000000 INFO @ Tue, 16 Jun 2020 08:05:56: 7000000 INFO @ Tue, 16 Jun 2020 08:05:59: 2000000 INFO @ Tue, 16 Jun 2020 08:06:01: 8000000 INFO @ Tue, 16 Jun 2020 08:06:04: 3000000 INFO @ Tue, 16 Jun 2020 08:06:06: 9000000 INFO @ Tue, 16 Jun 2020 08:06:08: 4000000 INFO @ Tue, 16 Jun 2020 08:06:12: 10000000 INFO @ Tue, 16 Jun 2020 08:06:13: 5000000 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 08:06:17: 11000000 INFO @ Tue, 16 Jun 2020 08:06:18: 6000000 INFO @ Tue, 16 Jun 2020 08:06:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228904/SRX2228904.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228904/SRX2228904.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228904/SRX2228904.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228904/SRX2228904.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 08:06:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:06:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:06:22: 12000000 INFO @ Tue, 16 Jun 2020 08:06:23: 7000000 INFO @ Tue, 16 Jun 2020 08:06:23: 1000000 INFO @ Tue, 16 Jun 2020 08:06:27: 13000000 INFO @ Tue, 16 Jun 2020 08:06:28: 8000000 INFO @ Tue, 16 Jun 2020 08:06:28: 2000000 INFO @ Tue, 16 Jun 2020 08:06:33: 14000000 INFO @ Tue, 16 Jun 2020 08:06:33: 9000000 INFO @ Tue, 16 Jun 2020 08:06:33: 3000000 INFO @ Tue, 16 Jun 2020 08:06:38: 10000000 INFO @ Tue, 16 Jun 2020 08:06:38: 15000000 INFO @ Tue, 16 Jun 2020 08:06:38: 4000000 INFO @ Tue, 16 Jun 2020 08:06:39: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:06:39: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:06:39: #1 total tags in treatment: 15200581 INFO @ Tue, 16 Jun 2020 08:06:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:06:39: #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 08:06:40: #1 tags after filtering in treatment: 15200581 INFO @ Tue, 16 Jun 2020 08:06:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:06:40: #1 finished! INFO @ Tue, 16 Jun 2020 08:06:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:06:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:06:41: #2 number of paired peaks: 266 WARNING @ Tue, 16 Jun 2020 08:06:41: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Tue, 16 Jun 2020 08:06:41: start model_add_line... INFO @ Tue, 16 Jun 2020 08:06:41: start X-correlation... INFO @ Tue, 16 Jun 2020 08:06:41: end of X-cor INFO @ Tue, 16 Jun 2020 08:06:41: #2 finished! INFO @ Tue, 16 Jun 2020 08:06:41: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 08:06:41: #2 alternative fragment length(s) may be 3,50 bps INFO @ Tue, 16 Jun 2020 08:06:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228904/SRX2228904.05_model.r WARNING @ Tue, 16 Jun 2020 08:06:41: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:06:41: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Tue, 16 Jun 2020 08:06:41: #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 08:06:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:06:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:06:42: 11000000 INFO @ Tue, 16 Jun 2020 08:06:43: 5000000 INFO @ Tue, 16 Jun 2020 08:06:47: 12000000 INFO @ Tue, 16 Jun 2020 08:06:48: 6000000 INFO @ Tue, 16 Jun 2020 08:06:52: 13000000 INFO @ Tue, 16 Jun 2020 08:06:53: 7000000 INFO @ Tue, 16 Jun 2020 08:06:57: 14000000 INFO @ Tue, 16 Jun 2020 08:06:58: 8000000 INFO @ Tue, 16 Jun 2020 08:07:02: 15000000 INFO @ Tue, 16 Jun 2020 08:07:03: 9000000 INFO @ Tue, 16 Jun 2020 08:07:03: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:07:03: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:07:03: #1 total tags in treatment: 15200581 INFO @ Tue, 16 Jun 2020 08:07:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:07:03: #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 08:07:03: #1 tags after filtering in treatment: 15200581 INFO @ Tue, 16 Jun 2020 08:07:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:07:03: #1 finished! INFO @ Tue, 16 Jun 2020 08:07:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:07:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:07:05: #2 number of paired peaks: 266 WARNING @ Tue, 16 Jun 2020 08:07:05: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Tue, 16 Jun 2020 08:07:05: start model_add_line... INFO @ Tue, 16 Jun 2020 08:07:05: start X-correlation... INFO @ Tue, 16 Jun 2020 08:07:05: end of X-cor INFO @ Tue, 16 Jun 2020 08:07:05: #2 finished! INFO @ Tue, 16 Jun 2020 08:07:05: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 08:07:05: #2 alternative fragment length(s) may be 3,50 bps INFO @ Tue, 16 Jun 2020 08:07:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228904/SRX2228904.10_model.r WARNING @ Tue, 16 Jun 2020 08:07:05: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:07:05: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Tue, 16 Jun 2020 08:07:05: #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 08:07:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:07:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:07:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:07:08: 10000000 INFO @ Tue, 16 Jun 2020 08:07:13: 11000000 INFO @ Tue, 16 Jun 2020 08:07:18: 12000000 INFO @ Tue, 16 Jun 2020 08:07:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228904/SRX2228904.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:07:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228904/SRX2228904.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:07:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228904/SRX2228904.05_summits.bed INFO @ Tue, 16 Jun 2020 08:07:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (685 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:07:22: 13000000 INFO @ Tue, 16 Jun 2020 08:07:27: 14000000 INFO @ Tue, 16 Jun 2020 08:07:32: 15000000 INFO @ Tue, 16 Jun 2020 08:07:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:07:33: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:07:33: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:07:33: #1 total tags in treatment: 15200581 INFO @ Tue, 16 Jun 2020 08:07:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:07:33: #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 08:07:34: #1 tags after filtering in treatment: 15200581 INFO @ Tue, 16 Jun 2020 08:07:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:07:34: #1 finished! INFO @ Tue, 16 Jun 2020 08:07:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:07:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:07:35: #2 number of paired peaks: 266 WARNING @ Tue, 16 Jun 2020 08:07:35: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Tue, 16 Jun 2020 08:07:35: start model_add_line... INFO @ Tue, 16 Jun 2020 08:07:35: start X-correlation... INFO @ Tue, 16 Jun 2020 08:07:35: end of X-cor INFO @ Tue, 16 Jun 2020 08:07:35: #2 finished! INFO @ Tue, 16 Jun 2020 08:07:35: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 08:07:35: #2 alternative fragment length(s) may be 3,50 bps INFO @ Tue, 16 Jun 2020 08:07:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228904/SRX2228904.20_model.r WARNING @ Tue, 16 Jun 2020 08:07:35: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:07:35: #2 You may need to consider one of the other alternative d(s): 3,50 WARNING @ Tue, 16 Jun 2020 08:07:35: #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 08:07:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:07:35: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:07:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228904/SRX2228904.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:07:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228904/SRX2228904.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:07:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228904/SRX2228904.10_summits.bed INFO @ Tue, 16 Jun 2020 08:07:47: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (427 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:08:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:08:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228904/SRX2228904.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:08:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228904/SRX2228904.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:08:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228904/SRX2228904.20_summits.bed INFO @ Tue, 16 Jun 2020 08:08:18: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (173 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。