Job ID = 6366316 SRX = SRX1132912 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:37:36 prefetch.2.10.7: 1) Downloading 'SRR2144361'... 2020-06-15T22:37:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:39:30 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:39:31 prefetch.2.10.7: 'SRR2144361' is valid 2020-06-15T22:39:31 prefetch.2.10.7: 1) 'SRR2144361' was downloaded successfully Read 14191303 spots for SRR2144361/SRR2144361.sra Written 14191303 spots for SRR2144361/SRR2144361.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: 00:03:54 14191303 reads; of these: 14191303 (100.00%) were unpaired; of these: 955869 (6.74%) aligned 0 times 11325571 (79.81%) aligned exactly 1 time 1909863 (13.46%) aligned >1 times 93.26% overall alignment rate Time searching: 00:03:54 Overall time: 00:03:54 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] 3316218 / 13235434 = 0.2506 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 07:48:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1132912/SRX1132912.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1132912/SRX1132912.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1132912/SRX1132912.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1132912/SRX1132912.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 07:48:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:48:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:48:21: 1000000 INFO @ Tue, 16 Jun 2020 07:48:26: 2000000 INFO @ Tue, 16 Jun 2020 07:48:32: 3000000 INFO @ Tue, 16 Jun 2020 07:48:37: 4000000 INFO @ Tue, 16 Jun 2020 07:48:43: 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 07:48:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1132912/SRX1132912.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1132912/SRX1132912.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1132912/SRX1132912.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1132912/SRX1132912.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 07:48:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:48:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:48:49: 6000000 INFO @ Tue, 16 Jun 2020 07:48:53: 1000000 INFO @ Tue, 16 Jun 2020 07:48:56: 7000000 INFO @ Tue, 16 Jun 2020 07:49:00: 2000000 INFO @ Tue, 16 Jun 2020 07:49:02: 8000000 INFO @ Tue, 16 Jun 2020 07:49:07: 3000000 INFO @ Tue, 16 Jun 2020 07:49:09: 9000000 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 07:49:14: 4000000 INFO @ Tue, 16 Jun 2020 07:49:15: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:49:15: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:49:15: #1 total tags in treatment: 9919216 INFO @ Tue, 16 Jun 2020 07:49:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:49:15: #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 07:49:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1132912/SRX1132912.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1132912/SRX1132912.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1132912/SRX1132912.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1132912/SRX1132912.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 07:49:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:49:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:49:15: #1 tags after filtering in treatment: 9919216 INFO @ Tue, 16 Jun 2020 07:49:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:49:15: #1 finished! INFO @ Tue, 16 Jun 2020 07:49:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:49:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:49:16: #2 number of paired peaks: 130 WARNING @ Tue, 16 Jun 2020 07:49:16: Fewer paired peaks (130) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 130 pairs to build model! INFO @ Tue, 16 Jun 2020 07:49:16: start model_add_line... INFO @ Tue, 16 Jun 2020 07:49:16: start X-correlation... INFO @ Tue, 16 Jun 2020 07:49:16: end of X-cor INFO @ Tue, 16 Jun 2020 07:49:16: #2 finished! INFO @ Tue, 16 Jun 2020 07:49:16: #2 predicted fragment length is 59 bps INFO @ Tue, 16 Jun 2020 07:49:16: #2 alternative fragment length(s) may be 1,59,132,135,204,522,571 bps INFO @ Tue, 16 Jun 2020 07:49:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1132912/SRX1132912.05_model.r WARNING @ Tue, 16 Jun 2020 07:49:16: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:49:16: #2 You may need to consider one of the other alternative d(s): 1,59,132,135,204,522,571 WARNING @ Tue, 16 Jun 2020 07:49:16: #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 07:49:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:49:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:49:21: 5000000 INFO @ Tue, 16 Jun 2020 07:49:22: 1000000 INFO @ Tue, 16 Jun 2020 07:49:29: 6000000 INFO @ Tue, 16 Jun 2020 07:49:29: 2000000 INFO @ Tue, 16 Jun 2020 07:49:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:49:36: 3000000 INFO @ Tue, 16 Jun 2020 07:49:36: 7000000 INFO @ Tue, 16 Jun 2020 07:49:43: 4000000 INFO @ Tue, 16 Jun 2020 07:49:43: 8000000 INFO @ Tue, 16 Jun 2020 07:49:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1132912/SRX1132912.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:49:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1132912/SRX1132912.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:49:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1132912/SRX1132912.05_summits.bed INFO @ Tue, 16 Jun 2020 07:49:44: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (417 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:49:49: 5000000 INFO @ Tue, 16 Jun 2020 07:49:50: 9000000 INFO @ Tue, 16 Jun 2020 07:49:56: 6000000 INFO @ Tue, 16 Jun 2020 07:49:57: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:49:57: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:49:57: #1 total tags in treatment: 9919216 INFO @ Tue, 16 Jun 2020 07:49:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:49:57: #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 07:49:57: #1 tags after filtering in treatment: 9919216 INFO @ Tue, 16 Jun 2020 07:49:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:49:57: #1 finished! INFO @ Tue, 16 Jun 2020 07:49:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:49:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:49:58: #2 number of paired peaks: 130 WARNING @ Tue, 16 Jun 2020 07:49:58: Fewer paired peaks (130) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 130 pairs to build model! INFO @ Tue, 16 Jun 2020 07:49:58: start model_add_line... INFO @ Tue, 16 Jun 2020 07:49:58: start X-correlation... INFO @ Tue, 16 Jun 2020 07:49:58: end of X-cor INFO @ Tue, 16 Jun 2020 07:49:58: #2 finished! INFO @ Tue, 16 Jun 2020 07:49:58: #2 predicted fragment length is 59 bps INFO @ Tue, 16 Jun 2020 07:49:58: #2 alternative fragment length(s) may be 1,59,132,135,204,522,571 bps INFO @ Tue, 16 Jun 2020 07:49:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1132912/SRX1132912.10_model.r WARNING @ Tue, 16 Jun 2020 07:49:58: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:49:58: #2 You may need to consider one of the other alternative d(s): 1,59,132,135,204,522,571 WARNING @ Tue, 16 Jun 2020 07:49:58: #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 07:49:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:49:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:50:03: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:50:09: 8000000 INFO @ Tue, 16 Jun 2020 07:50:15: 9000000 INFO @ Tue, 16 Jun 2020 07:50:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:50:20: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 07:50:20: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 07:50:20: #1 total tags in treatment: 9919216 INFO @ Tue, 16 Jun 2020 07:50:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:50:20: #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 07:50:21: #1 tags after filtering in treatment: 9919216 INFO @ Tue, 16 Jun 2020 07:50:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:50:21: #1 finished! INFO @ Tue, 16 Jun 2020 07:50:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:50:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:50:21: #2 number of paired peaks: 130 WARNING @ Tue, 16 Jun 2020 07:50:21: Fewer paired peaks (130) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 130 pairs to build model! INFO @ Tue, 16 Jun 2020 07:50:21: start model_add_line... INFO @ Tue, 16 Jun 2020 07:50:21: start X-correlation... INFO @ Tue, 16 Jun 2020 07:50:21: end of X-cor INFO @ Tue, 16 Jun 2020 07:50:21: #2 finished! INFO @ Tue, 16 Jun 2020 07:50:21: #2 predicted fragment length is 59 bps INFO @ Tue, 16 Jun 2020 07:50:21: #2 alternative fragment length(s) may be 1,59,132,135,204,522,571 bps INFO @ Tue, 16 Jun 2020 07:50:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1132912/SRX1132912.20_model.r WARNING @ Tue, 16 Jun 2020 07:50:21: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:50:21: #2 You may need to consider one of the other alternative d(s): 1,59,132,135,204,522,571 WARNING @ Tue, 16 Jun 2020 07:50:21: #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 07:50:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:50:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:50:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1132912/SRX1132912.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:50:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1132912/SRX1132912.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:50:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1132912/SRX1132912.10_summits.bed INFO @ Tue, 16 Jun 2020 07:50:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (146 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:50:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:50:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1132912/SRX1132912.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:50:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1132912/SRX1132912.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:50:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1132912/SRX1132912.20_summits.bed INFO @ Tue, 16 Jun 2020 07:50:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (23 records, 4 fields): 1 millis CompletedMACS2peakCalling