Job ID = 8070272 SRX = SRX8392426 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 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: 00:11:51 7620107 reads; of these: 7620107 (100.00%) were paired; of these: 2902462 (38.09%) aligned concordantly 0 times 4016450 (52.71%) aligned concordantly exactly 1 time 701195 (9.20%) aligned concordantly >1 times ---- 2902462 pairs aligned concordantly 0 times; of these: 965801 (33.28%) aligned discordantly 1 time ---- 1936661 pairs aligned 0 times concordantly or discordantly; of these: 3873322 mates make up the pairs; of these: 3563064 (91.99%) aligned 0 times 134483 (3.47%) aligned exactly 1 time 175775 (4.54%) aligned >1 times 76.62% overall alignment rate Time searching: 00:11:51 Overall time: 00:11:51 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 1057634 / 5633132 = 0.1878 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 @ Sat, 08 Aug 2020 13:18:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392426/SRX8392426.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392426/SRX8392426.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392426/SRX8392426.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392426/SRX8392426.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 @ Sat, 08 Aug 2020 13:18:48: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:18:48: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:18:55: 1000000 INFO @ Sat, 08 Aug 2020 13:19:02: 2000000 INFO @ Sat, 08 Aug 2020 13:19:09: 3000000 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 @ Sat, 08 Aug 2020 13:19:16: 4000000 INFO @ Sat, 08 Aug 2020 13:19:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392426/SRX8392426.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392426/SRX8392426.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392426/SRX8392426.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392426/SRX8392426.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 @ Sat, 08 Aug 2020 13:19:18: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:19:18: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:19:25: 5000000 INFO @ Sat, 08 Aug 2020 13:19:26: 1000000 INFO @ Sat, 08 Aug 2020 13:19:33: 6000000 INFO @ Sat, 08 Aug 2020 13:19:35: 2000000 INFO @ Sat, 08 Aug 2020 13:19:41: 7000000 INFO @ Sat, 08 Aug 2020 13:19:43: 3000000 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 @ Sat, 08 Aug 2020 13:19:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392426/SRX8392426.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392426/SRX8392426.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392426/SRX8392426.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392426/SRX8392426.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 @ Sat, 08 Aug 2020 13:19:48: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:19:48: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:19:50: 8000000 INFO @ Sat, 08 Aug 2020 13:19:52: 4000000 INFO @ Sat, 08 Aug 2020 13:19:56: 1000000 INFO @ Sat, 08 Aug 2020 13:19:58: 9000000 INFO @ Sat, 08 Aug 2020 13:20:00: 5000000 INFO @ Sat, 08 Aug 2020 13:20:03: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:20:03: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:20:03: #1 total tags in treatment: 3802571 INFO @ Sat, 08 Aug 2020 13:20:03: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:20:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:20:03: #1 tags after filtering in treatment: 3530609 INFO @ Sat, 08 Aug 2020 13:20:03: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 08 Aug 2020 13:20:03: #1 finished! INFO @ Sat, 08 Aug 2020 13:20:03: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:20:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:20:03: #2 number of paired peaks: 472 WARNING @ Sat, 08 Aug 2020 13:20:03: Fewer paired peaks (472) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 472 pairs to build model! INFO @ Sat, 08 Aug 2020 13:20:03: start model_add_line... INFO @ Sat, 08 Aug 2020 13:20:03: start X-correlation... INFO @ Sat, 08 Aug 2020 13:20:03: end of X-cor INFO @ Sat, 08 Aug 2020 13:20:03: #2 finished! INFO @ Sat, 08 Aug 2020 13:20:03: #2 predicted fragment length is 204 bps INFO @ Sat, 08 Aug 2020 13:20:03: #2 alternative fragment length(s) may be 204 bps INFO @ Sat, 08 Aug 2020 13:20:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392426/SRX8392426.05_model.r WARNING @ Sat, 08 Aug 2020 13:20:03: #2 Since the d (204) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:20:03: #2 You may need to consider one of the other alternative d(s): 204 WARNING @ Sat, 08 Aug 2020 13:20:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 13:20:03: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:20:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:20:04: 2000000 INFO @ Sat, 08 Aug 2020 13:20:09: 6000000 INFO @ Sat, 08 Aug 2020 13:20:11: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:20:13: 3000000 INFO @ Sat, 08 Aug 2020 13:20:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392426/SRX8392426.05_peaks.xls INFO @ Sat, 08 Aug 2020 13:20:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392426/SRX8392426.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:20:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392426/SRX8392426.05_summits.bed INFO @ Sat, 08 Aug 2020 13:20:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (360 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:20:17: 7000000 INFO @ Sat, 08 Aug 2020 13:20:21: 4000000 INFO @ Sat, 08 Aug 2020 13:20:26: 8000000 INFO @ Sat, 08 Aug 2020 13:20:29: 5000000 INFO @ Sat, 08 Aug 2020 13:20:34: 9000000 INFO @ Sat, 08 Aug 2020 13:20:37: 6000000 INFO @ Sat, 08 Aug 2020 13:20:38: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:20:38: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:20:38: #1 total tags in treatment: 3802571 INFO @ Sat, 08 Aug 2020 13:20:38: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:20:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:20:38: #1 tags after filtering in treatment: 3530609 INFO @ Sat, 08 Aug 2020 13:20:38: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 08 Aug 2020 13:20:38: #1 finished! INFO @ Sat, 08 Aug 2020 13:20:38: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:20:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:20:39: #2 number of paired peaks: 472 WARNING @ Sat, 08 Aug 2020 13:20:39: Fewer paired peaks (472) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 472 pairs to build model! INFO @ Sat, 08 Aug 2020 13:20:39: start model_add_line... INFO @ Sat, 08 Aug 2020 13:20:39: start X-correlation... INFO @ Sat, 08 Aug 2020 13:20:39: end of X-cor INFO @ Sat, 08 Aug 2020 13:20:39: #2 finished! INFO @ Sat, 08 Aug 2020 13:20:39: #2 predicted fragment length is 204 bps INFO @ Sat, 08 Aug 2020 13:20:39: #2 alternative fragment length(s) may be 204 bps INFO @ Sat, 08 Aug 2020 13:20:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392426/SRX8392426.10_model.r WARNING @ Sat, 08 Aug 2020 13:20:39: #2 Since the d (204) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:20:39: #2 You may need to consider one of the other alternative d(s): 204 WARNING @ Sat, 08 Aug 2020 13:20:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 13:20:39: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:20:39: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 13:20:45: 7000000 INFO @ Sat, 08 Aug 2020 13:20:47: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:20:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392426/SRX8392426.10_peaks.xls INFO @ Sat, 08 Aug 2020 13:20:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392426/SRX8392426.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:20:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392426/SRX8392426.10_summits.bed INFO @ Sat, 08 Aug 2020 13:20:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (246 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:20:53: 8000000 INFO @ Sat, 08 Aug 2020 13:21:00: 9000000 BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 13:21:05: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:21:05: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:21:05: #1 total tags in treatment: 3802571 INFO @ Sat, 08 Aug 2020 13:21:05: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:21:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:21:05: #1 tags after filtering in treatment: 3530609 INFO @ Sat, 08 Aug 2020 13:21:05: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 08 Aug 2020 13:21:05: #1 finished! INFO @ Sat, 08 Aug 2020 13:21:05: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:21:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:21:05: #2 number of paired peaks: 472 WARNING @ Sat, 08 Aug 2020 13:21:05: Fewer paired peaks (472) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 472 pairs to build model! INFO @ Sat, 08 Aug 2020 13:21:05: start model_add_line... INFO @ Sat, 08 Aug 2020 13:21:05: start X-correlation... INFO @ Sat, 08 Aug 2020 13:21:05: end of X-cor INFO @ Sat, 08 Aug 2020 13:21:05: #2 finished! INFO @ Sat, 08 Aug 2020 13:21:05: #2 predicted fragment length is 204 bps INFO @ Sat, 08 Aug 2020 13:21:05: #2 alternative fragment length(s) may be 204 bps INFO @ Sat, 08 Aug 2020 13:21:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392426/SRX8392426.20_model.r WARNING @ Sat, 08 Aug 2020 13:21:05: #2 Since the d (204) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:21:05: #2 You may need to consider one of the other alternative d(s): 204 WARNING @ Sat, 08 Aug 2020 13:21:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 13:21:05: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:21:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:21:13: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:21:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392426/SRX8392426.20_peaks.xls INFO @ Sat, 08 Aug 2020 13:21:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392426/SRX8392426.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:21:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392426/SRX8392426.20_summits.bed INFO @ Sat, 08 Aug 2020 13:21:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (165 records, 4 fields): 2 millis CompletedMACS2peakCalling