Job ID = 6507833 SRX = SRX494835 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T12:40:47 prefetch.2.10.7: 1) Downloading 'SRR1198367'... 2020-06-26T12:40:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T12:43:03 prefetch.2.10.7: HTTPS download succeed 2020-06-26T12:43:03 prefetch.2.10.7: 1) 'SRR1198367' was downloaded successfully Read 23497136 spots for SRR1198367/SRR1198367.sra Written 23497136 spots for SRR1198367/SRR1198367.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: 00:05:35 23497136 reads; of these: 23497136 (100.00%) were unpaired; of these: 270449 (1.15%) aligned 0 times 19082036 (81.21%) aligned exactly 1 time 4144651 (17.64%) aligned >1 times 98.85% overall alignment rate Time searching: 00:05:35 Overall time: 00:05:35 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] 9518209 / 23226687 = 0.4098 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 21:55:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494835/SRX494835.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494835/SRX494835.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494835/SRX494835.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494835/SRX494835.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 21:55:15: #1 read tag files... INFO @ Fri, 26 Jun 2020 21:55:15: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 21:55:20: 1000000 INFO @ Fri, 26 Jun 2020 21:55:25: 2000000 INFO @ Fri, 26 Jun 2020 21:55:31: 3000000 INFO @ Fri, 26 Jun 2020 21:55:36: 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 21:55:41: 5000000 INFO @ Fri, 26 Jun 2020 21:55:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494835/SRX494835.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494835/SRX494835.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494835/SRX494835.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494835/SRX494835.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 21:55:42: #1 read tag files... INFO @ Fri, 26 Jun 2020 21:55:42: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 21:55:47: 6000000 INFO @ Fri, 26 Jun 2020 21:55:48: 1000000 INFO @ Fri, 26 Jun 2020 21:55:52: 7000000 INFO @ Fri, 26 Jun 2020 21:55:53: 2000000 INFO @ Fri, 26 Jun 2020 21:55:58: 8000000 INFO @ Fri, 26 Jun 2020 21:55:59: 3000000 INFO @ Fri, 26 Jun 2020 21:56:03: 9000000 INFO @ Fri, 26 Jun 2020 21:56:04: 4000000 INFO @ Fri, 26 Jun 2020 21:56:09: 10000000 INFO @ Fri, 26 Jun 2020 21:56:10: 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 @ Fri, 26 Jun 2020 21:56:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494835/SRX494835.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494835/SRX494835.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494835/SRX494835.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494835/SRX494835.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 21:56:12: #1 read tag files... INFO @ Fri, 26 Jun 2020 21:56:12: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 21:56:14: 11000000 INFO @ Fri, 26 Jun 2020 21:56:15: 6000000 INFO @ Fri, 26 Jun 2020 21:56:18: 1000000 INFO @ Fri, 26 Jun 2020 21:56:20: 12000000 INFO @ Fri, 26 Jun 2020 21:56:21: 7000000 INFO @ Fri, 26 Jun 2020 21:56:23: 2000000 INFO @ Fri, 26 Jun 2020 21:56:25: 13000000 INFO @ Fri, 26 Jun 2020 21:56:26: 8000000 INFO @ Fri, 26 Jun 2020 21:56:29: 3000000 INFO @ Fri, 26 Jun 2020 21:56:29: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 21:56:29: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 21:56:29: #1 total tags in treatment: 13708478 INFO @ Fri, 26 Jun 2020 21:56:29: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 21:56:29: #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 21:56:30: #1 tags after filtering in treatment: 13708478 INFO @ Fri, 26 Jun 2020 21:56:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 21:56:30: #1 finished! INFO @ Fri, 26 Jun 2020 21:56:30: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 21:56:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 21:56:30: #2 number of paired peaks: 387 WARNING @ Fri, 26 Jun 2020 21:56:30: Fewer paired peaks (387) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 387 pairs to build model! INFO @ Fri, 26 Jun 2020 21:56:30: start model_add_line... INFO @ Fri, 26 Jun 2020 21:56:31: start X-correlation... INFO @ Fri, 26 Jun 2020 21:56:31: end of X-cor INFO @ Fri, 26 Jun 2020 21:56:31: #2 finished! INFO @ Fri, 26 Jun 2020 21:56:31: #2 predicted fragment length is 43 bps INFO @ Fri, 26 Jun 2020 21:56:31: #2 alternative fragment length(s) may be 2,43 bps INFO @ Fri, 26 Jun 2020 21:56:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494835/SRX494835.05_model.r WARNING @ Fri, 26 Jun 2020 21:56:31: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 21:56:31: #2 You may need to consider one of the other alternative d(s): 2,43 WARNING @ Fri, 26 Jun 2020 21:56:31: #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 21:56:31: #3 Call peaks... INFO @ Fri, 26 Jun 2020 21:56:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 21:56:32: 9000000 INFO @ Fri, 26 Jun 2020 21:56:34: 4000000 INFO @ Fri, 26 Jun 2020 21:56:37: 10000000 INFO @ Fri, 26 Jun 2020 21:56:40: 5000000 INFO @ Fri, 26 Jun 2020 21:56:43: 11000000 INFO @ Fri, 26 Jun 2020 21:56:45: 6000000 INFO @ Fri, 26 Jun 2020 21:56:48: 12000000 INFO @ Fri, 26 Jun 2020 21:56:51: 7000000 INFO @ Fri, 26 Jun 2020 21:56:54: 13000000 INFO @ Fri, 26 Jun 2020 21:56:56: 8000000 INFO @ Fri, 26 Jun 2020 21:56:57: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 21:56:57: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 21:56:57: #1 total tags in treatment: 13708478 INFO @ Fri, 26 Jun 2020 21:56:57: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 21:56:57: #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 21:56:57: #1 tags after filtering in treatment: 13708478 INFO @ Fri, 26 Jun 2020 21:56:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 21:56:57: #1 finished! INFO @ Fri, 26 Jun 2020 21:56:57: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 21:56:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 21:56:58: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 21:56:58: #2 number of paired peaks: 387 WARNING @ Fri, 26 Jun 2020 21:56:58: Fewer paired peaks (387) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 387 pairs to build model! INFO @ Fri, 26 Jun 2020 21:56:58: start model_add_line... INFO @ Fri, 26 Jun 2020 21:56:59: start X-correlation... INFO @ Fri, 26 Jun 2020 21:56:59: end of X-cor INFO @ Fri, 26 Jun 2020 21:56:59: #2 finished! INFO @ Fri, 26 Jun 2020 21:56:59: #2 predicted fragment length is 43 bps INFO @ Fri, 26 Jun 2020 21:56:59: #2 alternative fragment length(s) may be 2,43 bps INFO @ Fri, 26 Jun 2020 21:56:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494835/SRX494835.10_model.r WARNING @ Fri, 26 Jun 2020 21:56:59: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 21:56:59: #2 You may need to consider one of the other alternative d(s): 2,43 WARNING @ Fri, 26 Jun 2020 21:56:59: #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 21:56:59: #3 Call peaks... INFO @ Fri, 26 Jun 2020 21:56:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 21:57:01: 9000000 INFO @ Fri, 26 Jun 2020 21:57:07: 10000000 INFO @ Fri, 26 Jun 2020 21:57:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494835/SRX494835.05_peaks.xls INFO @ Fri, 26 Jun 2020 21:57:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494835/SRX494835.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 21:57:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494835/SRX494835.05_summits.bed INFO @ Fri, 26 Jun 2020 21:57:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (819 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 21:57:12: 11000000 INFO @ Fri, 26 Jun 2020 21:57:17: 12000000 INFO @ Fri, 26 Jun 2020 21:57:22: 13000000 INFO @ Fri, 26 Jun 2020 21:57:25: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 21:57:26: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 21:57:26: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 21:57:26: #1 total tags in treatment: 13708478 INFO @ Fri, 26 Jun 2020 21:57:26: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 21:57:26: #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 21:57:26: #1 tags after filtering in treatment: 13708478 INFO @ Fri, 26 Jun 2020 21:57:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 21:57:26: #1 finished! INFO @ Fri, 26 Jun 2020 21:57:26: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 21:57:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 21:57:27: #2 number of paired peaks: 387 WARNING @ Fri, 26 Jun 2020 21:57:27: Fewer paired peaks (387) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 387 pairs to build model! INFO @ Fri, 26 Jun 2020 21:57:27: start model_add_line... INFO @ Fri, 26 Jun 2020 21:57:27: start X-correlation... INFO @ Fri, 26 Jun 2020 21:57:27: end of X-cor INFO @ Fri, 26 Jun 2020 21:57:27: #2 finished! INFO @ Fri, 26 Jun 2020 21:57:27: #2 predicted fragment length is 43 bps INFO @ Fri, 26 Jun 2020 21:57:27: #2 alternative fragment length(s) may be 2,43 bps INFO @ Fri, 26 Jun 2020 21:57:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494835/SRX494835.20_model.r WARNING @ Fri, 26 Jun 2020 21:57:27: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 21:57:27: #2 You may need to consider one of the other alternative d(s): 2,43 WARNING @ Fri, 26 Jun 2020 21:57:27: #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 21:57:27: #3 Call peaks... INFO @ Fri, 26 Jun 2020 21:57:27: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 21:57:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494835/SRX494835.10_peaks.xls INFO @ Fri, 26 Jun 2020 21:57:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494835/SRX494835.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 21:57:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494835/SRX494835.10_summits.bed INFO @ Fri, 26 Jun 2020 21:57:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (539 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 21:57:54: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 21:58:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494835/SRX494835.20_peaks.xls INFO @ Fri, 26 Jun 2020 21:58:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494835/SRX494835.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 21:58:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494835/SRX494835.20_summits.bed INFO @ Fri, 26 Jun 2020 21:58:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (207 records, 4 fields): 1 millis CompletedMACS2peakCalling