Job ID = 8070297 SRX = SRX7217778 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: 00:14:04 7928426 reads; of these: 7928426 (100.00%) were paired; of these: 1780463 (22.46%) aligned concordantly 0 times 5308774 (66.96%) aligned concordantly exactly 1 time 839189 (10.58%) aligned concordantly >1 times ---- 1780463 pairs aligned concordantly 0 times; of these: 572214 (32.14%) aligned discordantly 1 time ---- 1208249 pairs aligned 0 times concordantly or discordantly; of these: 2416498 mates make up the pairs; of these: 2173086 (89.93%) aligned 0 times 133685 (5.53%) aligned exactly 1 time 109727 (4.54%) aligned >1 times 86.30% overall alignment rate Time searching: 00:14:04 Overall time: 00:14:04 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] 969066 / 6680756 = 0.1451 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 13:22:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7217778/SRX7217778.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7217778/SRX7217778.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7217778/SRX7217778.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7217778/SRX7217778.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 13:22:03: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:22:03: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:22:11: 1000000 INFO @ Sat, 08 Aug 2020 13:22:19: 2000000 INFO @ Sat, 08 Aug 2020 13:22:28: 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 13:22:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7217778/SRX7217778.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7217778/SRX7217778.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7217778/SRX7217778.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7217778/SRX7217778.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 13:22:34: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:22:34: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:22:36: 4000000 INFO @ Sat, 08 Aug 2020 13:22:43: 1000000 INFO @ Sat, 08 Aug 2020 13:22:46: 5000000 INFO @ Sat, 08 Aug 2020 13:22:53: 2000000 INFO @ Sat, 08 Aug 2020 13:22:55: 6000000 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 13:23:02: 3000000 INFO @ Sat, 08 Aug 2020 13:23:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7217778/SRX7217778.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7217778/SRX7217778.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7217778/SRX7217778.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7217778/SRX7217778.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 13:23:03: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:23:03: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:23:04: 7000000 INFO @ Sat, 08 Aug 2020 13:23:12: 4000000 INFO @ Sat, 08 Aug 2020 13:23:14: 1000000 INFO @ Sat, 08 Aug 2020 13:23:15: 8000000 INFO @ Sat, 08 Aug 2020 13:23:22: 5000000 INFO @ Sat, 08 Aug 2020 13:23:25: 2000000 INFO @ Sat, 08 Aug 2020 13:23:26: 9000000 INFO @ Sat, 08 Aug 2020 13:23:33: 6000000 INFO @ Sat, 08 Aug 2020 13:23:36: 10000000 INFO @ Sat, 08 Aug 2020 13:23:37: 3000000 INFO @ Sat, 08 Aug 2020 13:23:43: 7000000 INFO @ Sat, 08 Aug 2020 13:23:46: 11000000 INFO @ Sat, 08 Aug 2020 13:23:48: 4000000 INFO @ Sat, 08 Aug 2020 13:23:54: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:23:54: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:23:54: #1 total tags in treatment: 5245494 INFO @ Sat, 08 Aug 2020 13:23:54: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:23:54: #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 13:23:54: #1 tags after filtering in treatment: 4837044 INFO @ Sat, 08 Aug 2020 13:23:54: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 08 Aug 2020 13:23:54: #1 finished! INFO @ Sat, 08 Aug 2020 13:23:54: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:23:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:23:54: 8000000 INFO @ Sat, 08 Aug 2020 13:23:54: #2 number of paired peaks: 420 WARNING @ Sat, 08 Aug 2020 13:23:54: Fewer paired peaks (420) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 420 pairs to build model! INFO @ Sat, 08 Aug 2020 13:23:54: start model_add_line... INFO @ Sat, 08 Aug 2020 13:23:55: start X-correlation... INFO @ Sat, 08 Aug 2020 13:23:55: end of X-cor INFO @ Sat, 08 Aug 2020 13:23:55: #2 finished! INFO @ Sat, 08 Aug 2020 13:23:55: #2 predicted fragment length is 209 bps INFO @ Sat, 08 Aug 2020 13:23:55: #2 alternative fragment length(s) may be 209 bps INFO @ Sat, 08 Aug 2020 13:23:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7217778/SRX7217778.05_model.r WARNING @ Sat, 08 Aug 2020 13:23:55: #2 Since the d (209) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:23:55: #2 You may need to consider one of the other alternative d(s): 209 WARNING @ Sat, 08 Aug 2020 13:23:55: #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 13:23:55: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:23:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:24:00: 5000000 INFO @ Sat, 08 Aug 2020 13:24:05: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:24:05: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 13:24:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7217778/SRX7217778.05_peaks.xls INFO @ Sat, 08 Aug 2020 13:24:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7217778/SRX7217778.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:24:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7217778/SRX7217778.05_summits.bed INFO @ Sat, 08 Aug 2020 13:24:10: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (306 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:24:11: 6000000 INFO @ Sat, 08 Aug 2020 13:24:16: 10000000 INFO @ Sat, 08 Aug 2020 13:24:23: 7000000 INFO @ Sat, 08 Aug 2020 13:24:26: 11000000 BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 13:24:33: 8000000 INFO @ Sat, 08 Aug 2020 13:24:35: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:24:35: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:24:35: #1 total tags in treatment: 5245494 INFO @ Sat, 08 Aug 2020 13:24:35: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:24:35: #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 13:24:35: #1 tags after filtering in treatment: 4837044 INFO @ Sat, 08 Aug 2020 13:24:35: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 08 Aug 2020 13:24:35: #1 finished! INFO @ Sat, 08 Aug 2020 13:24:35: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:24:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:24:35: #2 number of paired peaks: 420 WARNING @ Sat, 08 Aug 2020 13:24:35: Fewer paired peaks (420) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 420 pairs to build model! INFO @ Sat, 08 Aug 2020 13:24:35: start model_add_line... INFO @ Sat, 08 Aug 2020 13:24:35: start X-correlation... INFO @ Sat, 08 Aug 2020 13:24:35: end of X-cor INFO @ Sat, 08 Aug 2020 13:24:35: #2 finished! INFO @ Sat, 08 Aug 2020 13:24:35: #2 predicted fragment length is 209 bps INFO @ Sat, 08 Aug 2020 13:24:35: #2 alternative fragment length(s) may be 209 bps INFO @ Sat, 08 Aug 2020 13:24:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7217778/SRX7217778.10_model.r WARNING @ Sat, 08 Aug 2020 13:24:35: #2 Since the d (209) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:24:35: #2 You may need to consider one of the other alternative d(s): 209 WARNING @ Sat, 08 Aug 2020 13:24:35: #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 13:24:35: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:24:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:24:44: 9000000 INFO @ Sat, 08 Aug 2020 13:24:46: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:24:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7217778/SRX7217778.10_peaks.xls INFO @ Sat, 08 Aug 2020 13:24:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7217778/SRX7217778.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:24:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7217778/SRX7217778.10_summits.bed INFO @ Sat, 08 Aug 2020 13:24:51: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (228 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:24:55: 10000000 INFO @ Sat, 08 Aug 2020 13:25:06: 11000000 INFO @ Sat, 08 Aug 2020 13:25:13: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:25:13: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:25:13: #1 total tags in treatment: 5245494 INFO @ Sat, 08 Aug 2020 13:25:13: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:25:13: #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 13:25:13: #1 tags after filtering in treatment: 4837044 INFO @ Sat, 08 Aug 2020 13:25:13: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 08 Aug 2020 13:25:13: #1 finished! INFO @ Sat, 08 Aug 2020 13:25:13: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:25:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:25:14: #2 number of paired peaks: 420 WARNING @ Sat, 08 Aug 2020 13:25:14: Fewer paired peaks (420) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 420 pairs to build model! INFO @ Sat, 08 Aug 2020 13:25:14: start model_add_line... INFO @ Sat, 08 Aug 2020 13:25:14: start X-correlation... INFO @ Sat, 08 Aug 2020 13:25:14: end of X-cor INFO @ Sat, 08 Aug 2020 13:25:14: #2 finished! INFO @ Sat, 08 Aug 2020 13:25:14: #2 predicted fragment length is 209 bps INFO @ Sat, 08 Aug 2020 13:25:14: #2 alternative fragment length(s) may be 209 bps INFO @ Sat, 08 Aug 2020 13:25:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7217778/SRX7217778.20_model.r WARNING @ Sat, 08 Aug 2020 13:25:14: #2 Since the d (209) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:25:14: #2 You may need to consider one of the other alternative d(s): 209 WARNING @ Sat, 08 Aug 2020 13:25:14: #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 13:25:14: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:25:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:25:24: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:25:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7217778/SRX7217778.20_peaks.xls INFO @ Sat, 08 Aug 2020 13:25:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7217778/SRX7217778.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:25:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7217778/SRX7217778.20_summits.bed INFO @ Sat, 08 Aug 2020 13:25:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (168 records, 4 fields): 1 millis CompletedMACS2peakCalling