Job ID = 6507850 SRX = SRX494934 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:03:48 prefetch.2.10.7: 1) Downloading 'SRR1198466'... 2020-06-26T13:03:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:06:38 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:06:38 prefetch.2.10.7: 1) 'SRR1198466' was downloaded successfully Read 26578904 spots for SRR1198466/SRR1198466.sra Written 26578904 spots for SRR1198466/SRR1198466.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: 00:06:23 26578904 reads; of these: 26578904 (100.00%) were unpaired; of these: 1723702 (6.49%) aligned 0 times 21432676 (80.64%) aligned exactly 1 time 3422526 (12.88%) aligned >1 times 93.51% overall alignment rate Time searching: 00:06:23 Overall time: 00:06:23 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 12 files... [bam_rmdupse_core] 13208955 / 24855202 = 0.5314 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 @ Fri, 26 Jun 2020 22:19:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494934/SRX494934.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494934/SRX494934.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494934/SRX494934.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494934/SRX494934.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 @ Fri, 26 Jun 2020 22:19:47: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:19:47: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:19:54: 1000000 INFO @ Fri, 26 Jun 2020 22:20:00: 2000000 INFO @ Fri, 26 Jun 2020 22:20:06: 3000000 INFO @ Fri, 26 Jun 2020 22:20:12: 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 @ Fri, 26 Jun 2020 22:20:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494934/SRX494934.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494934/SRX494934.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494934/SRX494934.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494934/SRX494934.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 @ Fri, 26 Jun 2020 22:20:17: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:20:17: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:20:18: 5000000 INFO @ Fri, 26 Jun 2020 22:20:24: 1000000 INFO @ Fri, 26 Jun 2020 22:20:25: 6000000 INFO @ Fri, 26 Jun 2020 22:20:31: 7000000 INFO @ Fri, 26 Jun 2020 22:20:31: 2000000 INFO @ Fri, 26 Jun 2020 22:20:38: 8000000 INFO @ Fri, 26 Jun 2020 22:20:38: 3000000 INFO @ Fri, 26 Jun 2020 22:20:45: 9000000 INFO @ Fri, 26 Jun 2020 22:20:45: 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 @ Fri, 26 Jun 2020 22:20:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494934/SRX494934.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494934/SRX494934.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494934/SRX494934.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494934/SRX494934.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 @ Fri, 26 Jun 2020 22:20:48: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:20:48: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:20:52: 10000000 INFO @ Fri, 26 Jun 2020 22:20:52: 5000000 INFO @ Fri, 26 Jun 2020 22:20:54: 1000000 INFO @ Fri, 26 Jun 2020 22:20:59: 11000000 INFO @ Fri, 26 Jun 2020 22:20:59: 6000000 INFO @ Fri, 26 Jun 2020 22:21:01: 2000000 INFO @ Fri, 26 Jun 2020 22:21:03: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:21:03: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:21:03: #1 total tags in treatment: 11646247 INFO @ Fri, 26 Jun 2020 22:21:03: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:21:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:21:03: #1 tags after filtering in treatment: 11646247 INFO @ Fri, 26 Jun 2020 22:21:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:21:03: #1 finished! INFO @ Fri, 26 Jun 2020 22:21:03: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:21:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:21:04: #2 number of paired peaks: 307 WARNING @ Fri, 26 Jun 2020 22:21:04: Fewer paired peaks (307) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 307 pairs to build model! INFO @ Fri, 26 Jun 2020 22:21:04: start model_add_line... INFO @ Fri, 26 Jun 2020 22:21:04: start X-correlation... INFO @ Fri, 26 Jun 2020 22:21:04: end of X-cor INFO @ Fri, 26 Jun 2020 22:21:04: #2 finished! INFO @ Fri, 26 Jun 2020 22:21:04: #2 predicted fragment length is 46 bps INFO @ Fri, 26 Jun 2020 22:21:04: #2 alternative fragment length(s) may be 2,46,538 bps INFO @ Fri, 26 Jun 2020 22:21:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494934/SRX494934.05_model.r WARNING @ Fri, 26 Jun 2020 22:21:04: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:21:04: #2 You may need to consider one of the other alternative d(s): 2,46,538 WARNING @ Fri, 26 Jun 2020 22:21:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:21:04: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:21:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:21:06: 7000000 INFO @ Fri, 26 Jun 2020 22:21:08: 3000000 INFO @ Fri, 26 Jun 2020 22:21:13: 8000000 INFO @ Fri, 26 Jun 2020 22:21:15: 4000000 INFO @ Fri, 26 Jun 2020 22:21:20: 9000000 INFO @ Fri, 26 Jun 2020 22:21:22: 5000000 INFO @ Fri, 26 Jun 2020 22:21:27: 10000000 INFO @ Fri, 26 Jun 2020 22:21:28: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:21:29: 6000000 INFO @ Fri, 26 Jun 2020 22:21:34: 11000000 INFO @ Fri, 26 Jun 2020 22:21:36: 7000000 INFO @ Fri, 26 Jun 2020 22:21:38: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:21:38: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:21:38: #1 total tags in treatment: 11646247 INFO @ Fri, 26 Jun 2020 22:21:38: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:21:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:21:38: #1 tags after filtering in treatment: 11646247 INFO @ Fri, 26 Jun 2020 22:21:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:21:38: #1 finished! INFO @ Fri, 26 Jun 2020 22:21:38: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:21:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:21:39: #2 number of paired peaks: 307 WARNING @ Fri, 26 Jun 2020 22:21:39: Fewer paired peaks (307) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 307 pairs to build model! INFO @ Fri, 26 Jun 2020 22:21:39: start model_add_line... INFO @ Fri, 26 Jun 2020 22:21:39: start X-correlation... INFO @ Fri, 26 Jun 2020 22:21:39: end of X-cor INFO @ Fri, 26 Jun 2020 22:21:39: #2 finished! INFO @ Fri, 26 Jun 2020 22:21:39: #2 predicted fragment length is 46 bps INFO @ Fri, 26 Jun 2020 22:21:39: #2 alternative fragment length(s) may be 2,46,538 bps INFO @ Fri, 26 Jun 2020 22:21:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494934/SRX494934.10_model.r WARNING @ Fri, 26 Jun 2020 22:21:39: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:21:39: #2 You may need to consider one of the other alternative d(s): 2,46,538 WARNING @ Fri, 26 Jun 2020 22:21:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:21:39: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:21:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:21:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494934/SRX494934.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:21:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494934/SRX494934.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:21:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494934/SRX494934.05_summits.bed INFO @ Fri, 26 Jun 2020 22:21:40: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (675 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:21:42: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:21:49: 9000000 INFO @ Fri, 26 Jun 2020 22:21:55: 10000000 INFO @ Fri, 26 Jun 2020 22:22:01: 11000000 INFO @ Fri, 26 Jun 2020 22:22:03: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:22:05: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:22:05: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:22:05: #1 total tags in treatment: 11646247 INFO @ Fri, 26 Jun 2020 22:22:05: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:22:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:22:05: #1 tags after filtering in treatment: 11646247 INFO @ Fri, 26 Jun 2020 22:22:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:22:05: #1 finished! INFO @ Fri, 26 Jun 2020 22:22:05: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:22:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:22:06: #2 number of paired peaks: 307 WARNING @ Fri, 26 Jun 2020 22:22:06: Fewer paired peaks (307) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 307 pairs to build model! INFO @ Fri, 26 Jun 2020 22:22:06: start model_add_line... INFO @ Fri, 26 Jun 2020 22:22:06: start X-correlation... INFO @ Fri, 26 Jun 2020 22:22:06: end of X-cor INFO @ Fri, 26 Jun 2020 22:22:06: #2 finished! INFO @ Fri, 26 Jun 2020 22:22:06: #2 predicted fragment length is 46 bps INFO @ Fri, 26 Jun 2020 22:22:06: #2 alternative fragment length(s) may be 2,46,538 bps INFO @ Fri, 26 Jun 2020 22:22:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494934/SRX494934.20_model.r WARNING @ Fri, 26 Jun 2020 22:22:06: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:22:06: #2 You may need to consider one of the other alternative d(s): 2,46,538 WARNING @ Fri, 26 Jun 2020 22:22:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:22:06: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:22:06: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:22:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494934/SRX494934.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:22:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494934/SRX494934.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:22:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494934/SRX494934.10_summits.bed INFO @ Fri, 26 Jun 2020 22:22:15: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (402 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:22:29: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:22:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494934/SRX494934.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:22:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494934/SRX494934.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:22:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494934/SRX494934.20_summits.bed INFO @ Fri, 26 Jun 2020 22:22:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (163 records, 4 fields): 1 millis CompletedMACS2peakCalling