Job ID = 6367662 SRX = SRX3733156 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:31:50 prefetch.2.10.7: 1) Downloading 'SRR6760669'... 2020-06-15T23:31:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:42:34 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:42:34 prefetch.2.10.7: 1) 'SRR6760669' was downloaded successfully 2020-06-15T23:42:34 prefetch.2.10.7: 'SRR6760669' has 0 unresolved dependencies Read 25826866 spots for SRR6760669/SRR6760669.sra Written 25826866 spots for SRR6760669/SRR6760669.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: 00:33:08 25826866 reads; of these: 25826866 (100.00%) were paired; of these: 3302869 (12.79%) aligned concordantly 0 times 19996371 (77.42%) aligned concordantly exactly 1 time 2527626 (9.79%) aligned concordantly >1 times ---- 3302869 pairs aligned concordantly 0 times; of these: 855370 (25.90%) aligned discordantly 1 time ---- 2447499 pairs aligned 0 times concordantly or discordantly; of these: 4894998 mates make up the pairs; of these: 3991253 (81.54%) aligned 0 times 562558 (11.49%) aligned exactly 1 time 341187 (6.97%) aligned >1 times 92.27% overall alignment rate Time searching: 00:33:08 Overall time: 00:33:08 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 20 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] 15666398 / 23286075 = 0.6728 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 09:29:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3733156/SRX3733156.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3733156/SRX3733156.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3733156/SRX3733156.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3733156/SRX3733156.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 09:29:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:29:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:29:55: 1000000 INFO @ Tue, 16 Jun 2020 09:30:02: 2000000 INFO @ Tue, 16 Jun 2020 09:30:09: 3000000 INFO @ Tue, 16 Jun 2020 09:30:15: 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 @ Tue, 16 Jun 2020 09:30:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3733156/SRX3733156.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3733156/SRX3733156.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3733156/SRX3733156.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3733156/SRX3733156.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 09:30:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:30:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:30:22: 5000000 INFO @ Tue, 16 Jun 2020 09:30:26: 1000000 INFO @ Tue, 16 Jun 2020 09:30:30: 6000000 INFO @ Tue, 16 Jun 2020 09:30:34: 2000000 INFO @ Tue, 16 Jun 2020 09:30:37: 7000000 INFO @ Tue, 16 Jun 2020 09:30:42: 3000000 INFO @ Tue, 16 Jun 2020 09:30:45: 8000000 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 09:30:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3733156/SRX3733156.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3733156/SRX3733156.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3733156/SRX3733156.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3733156/SRX3733156.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 09:30:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:30:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:30:49: 4000000 INFO @ Tue, 16 Jun 2020 09:30:52: 9000000 INFO @ Tue, 16 Jun 2020 09:30:56: 1000000 INFO @ Tue, 16 Jun 2020 09:30:57: 5000000 INFO @ Tue, 16 Jun 2020 09:31:00: 10000000 INFO @ Tue, 16 Jun 2020 09:31:04: 2000000 INFO @ Tue, 16 Jun 2020 09:31:04: 6000000 INFO @ Tue, 16 Jun 2020 09:31:07: 11000000 INFO @ Tue, 16 Jun 2020 09:31:11: 3000000 INFO @ Tue, 16 Jun 2020 09:31:12: 7000000 INFO @ Tue, 16 Jun 2020 09:31:14: 12000000 INFO @ Tue, 16 Jun 2020 09:31:19: 4000000 INFO @ Tue, 16 Jun 2020 09:31:20: 8000000 INFO @ Tue, 16 Jun 2020 09:31:22: 13000000 INFO @ Tue, 16 Jun 2020 09:31:26: 5000000 INFO @ Tue, 16 Jun 2020 09:31:27: 9000000 INFO @ Tue, 16 Jun 2020 09:31:30: 14000000 INFO @ Tue, 16 Jun 2020 09:31:34: 6000000 INFO @ Tue, 16 Jun 2020 09:31:35: 10000000 INFO @ Tue, 16 Jun 2020 09:31:37: 15000000 INFO @ Tue, 16 Jun 2020 09:31:41: 7000000 INFO @ Tue, 16 Jun 2020 09:31:43: 11000000 INFO @ Tue, 16 Jun 2020 09:31:45: 16000000 INFO @ Tue, 16 Jun 2020 09:31:48: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:31:48: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:31:48: #1 total tags in treatment: 7310195 INFO @ Tue, 16 Jun 2020 09:31:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:31:48: #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 09:31:48: #1 tags after filtering in treatment: 5981692 INFO @ Tue, 16 Jun 2020 09:31:48: #1 Redundant rate of treatment: 0.18 INFO @ Tue, 16 Jun 2020 09:31:48: #1 finished! INFO @ Tue, 16 Jun 2020 09:31:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:31:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:31:48: #2 number of paired peaks: 628 WARNING @ Tue, 16 Jun 2020 09:31:48: Fewer paired peaks (628) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 628 pairs to build model! INFO @ Tue, 16 Jun 2020 09:31:48: start model_add_line... INFO @ Tue, 16 Jun 2020 09:31:48: start X-correlation... INFO @ Tue, 16 Jun 2020 09:31:48: end of X-cor INFO @ Tue, 16 Jun 2020 09:31:48: #2 finished! INFO @ Tue, 16 Jun 2020 09:31:48: #2 predicted fragment length is 163 bps INFO @ Tue, 16 Jun 2020 09:31:48: #2 alternative fragment length(s) may be 163 bps INFO @ Tue, 16 Jun 2020 09:31:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3733156/SRX3733156.05_model.r INFO @ Tue, 16 Jun 2020 09:31:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:31:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:31:49: 8000000 INFO @ Tue, 16 Jun 2020 09:31:50: 12000000 INFO @ Tue, 16 Jun 2020 09:31:56: 9000000 INFO @ Tue, 16 Jun 2020 09:31:58: 13000000 INFO @ Tue, 16 Jun 2020 09:32:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:32:04: 10000000 INFO @ Tue, 16 Jun 2020 09:32:05: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:32:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3733156/SRX3733156.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:32:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3733156/SRX3733156.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:32:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3733156/SRX3733156.05_summits.bed INFO @ Tue, 16 Jun 2020 09:32:10: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (519 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:32:11: 11000000 INFO @ Tue, 16 Jun 2020 09:32:13: 15000000 INFO @ Tue, 16 Jun 2020 09:32:19: 12000000 INFO @ Tue, 16 Jun 2020 09:32:21: 16000000 INFO @ Tue, 16 Jun 2020 09:32:23: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:32:23: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:32:23: #1 total tags in treatment: 7310195 INFO @ Tue, 16 Jun 2020 09:32:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:32:23: #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 09:32:23: #1 tags after filtering in treatment: 5981692 INFO @ Tue, 16 Jun 2020 09:32:23: #1 Redundant rate of treatment: 0.18 INFO @ Tue, 16 Jun 2020 09:32:23: #1 finished! INFO @ Tue, 16 Jun 2020 09:32:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:32:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:32:24: #2 number of paired peaks: 628 WARNING @ Tue, 16 Jun 2020 09:32:24: Fewer paired peaks (628) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 628 pairs to build model! INFO @ Tue, 16 Jun 2020 09:32:24: start model_add_line... INFO @ Tue, 16 Jun 2020 09:32:24: start X-correlation... INFO @ Tue, 16 Jun 2020 09:32:24: end of X-cor INFO @ Tue, 16 Jun 2020 09:32:24: #2 finished! INFO @ Tue, 16 Jun 2020 09:32:24: #2 predicted fragment length is 163 bps INFO @ Tue, 16 Jun 2020 09:32:24: #2 alternative fragment length(s) may be 163 bps INFO @ Tue, 16 Jun 2020 09:32:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3733156/SRX3733156.10_model.r INFO @ Tue, 16 Jun 2020 09:32:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:32:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:32:26: 13000000 INFO @ Tue, 16 Jun 2020 09:32:33: 14000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:32:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:32:40: 15000000 INFO @ Tue, 16 Jun 2020 09:32:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3733156/SRX3733156.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:32:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3733156/SRX3733156.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:32:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3733156/SRX3733156.10_summits.bed INFO @ Tue, 16 Jun 2020 09:32:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (362 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:32:47: 16000000 INFO @ Tue, 16 Jun 2020 09:32:49: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:32:49: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:32:49: #1 total tags in treatment: 7310195 INFO @ Tue, 16 Jun 2020 09:32:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:32:49: #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 09:32:49: #1 tags after filtering in treatment: 5981692 INFO @ Tue, 16 Jun 2020 09:32:49: #1 Redundant rate of treatment: 0.18 INFO @ Tue, 16 Jun 2020 09:32:49: #1 finished! INFO @ Tue, 16 Jun 2020 09:32:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:32:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:32:50: #2 number of paired peaks: 628 WARNING @ Tue, 16 Jun 2020 09:32:50: Fewer paired peaks (628) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 628 pairs to build model! INFO @ Tue, 16 Jun 2020 09:32:50: start model_add_line... INFO @ Tue, 16 Jun 2020 09:32:50: start X-correlation... INFO @ Tue, 16 Jun 2020 09:32:50: end of X-cor INFO @ Tue, 16 Jun 2020 09:32:50: #2 finished! INFO @ Tue, 16 Jun 2020 09:32:50: #2 predicted fragment length is 163 bps INFO @ Tue, 16 Jun 2020 09:32:50: #2 alternative fragment length(s) may be 163 bps INFO @ Tue, 16 Jun 2020 09:32:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3733156/SRX3733156.20_model.r INFO @ Tue, 16 Jun 2020 09:32:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:32:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:33:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:33:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3733156/SRX3733156.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:33:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3733156/SRX3733156.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:33:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3733156/SRX3733156.20_summits.bed INFO @ Tue, 16 Jun 2020 09:33:13: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (233 records, 4 fields): 2 millis CompletedMACS2peakCalling