Job ID = 6367805 SRX = SRX4085373 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:48:33 prefetch.2.10.7: 1) Downloading 'SRR7167402'... 2020-06-15T23:48:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:53:21 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:53:21 prefetch.2.10.7: 1) 'SRR7167402' was downloaded successfully Read 13330407 spots for SRR7167402/SRR7167402.sra Written 13330407 spots for SRR7167402/SRR7167402.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: 00:09:15 13330407 reads; of these: 13330407 (100.00%) were paired; of these: 7119417 (53.41%) aligned concordantly 0 times 5366833 (40.26%) aligned concordantly exactly 1 time 844157 (6.33%) aligned concordantly >1 times ---- 7119417 pairs aligned concordantly 0 times; of these: 303297 (4.26%) aligned discordantly 1 time ---- 6816120 pairs aligned 0 times concordantly or discordantly; of these: 13632240 mates make up the pairs; of these: 11108094 (81.48%) aligned 0 times 2156395 (15.82%) aligned exactly 1 time 367751 (2.70%) aligned >1 times 58.34% overall alignment rate Time searching: 00:09:15 Overall time: 00:09:15 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_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] 534539 / 6400604 = 0.0835 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 09:10:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085373/SRX4085373.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085373/SRX4085373.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085373/SRX4085373.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085373/SRX4085373.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 09:10:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:11: 1000000 INFO @ Tue, 16 Jun 2020 09:10:17: 2000000 INFO @ Tue, 16 Jun 2020 09:10:24: 3000000 INFO @ Tue, 16 Jun 2020 09:10:30: 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 09:10:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085373/SRX4085373.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085373/SRX4085373.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085373/SRX4085373.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085373/SRX4085373.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 09:10:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:37: 5000000 INFO @ Tue, 16 Jun 2020 09:10:41: 1000000 INFO @ Tue, 16 Jun 2020 09:10:43: 6000000 INFO @ Tue, 16 Jun 2020 09:10:47: 2000000 INFO @ Tue, 16 Jun 2020 09:10:50: 7000000 INFO @ Tue, 16 Jun 2020 09:10:53: 3000000 INFO @ Tue, 16 Jun 2020 09:10:56: 8000000 INFO @ Tue, 16 Jun 2020 09:11:00: 4000000 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 09:11:02: 9000000 INFO @ Tue, 16 Jun 2020 09:11:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085373/SRX4085373.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085373/SRX4085373.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085373/SRX4085373.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085373/SRX4085373.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 09:11:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:11:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:11:06: 5000000 INFO @ Tue, 16 Jun 2020 09:11:09: 10000000 INFO @ Tue, 16 Jun 2020 09:11:11: 1000000 INFO @ Tue, 16 Jun 2020 09:11:13: 6000000 INFO @ Tue, 16 Jun 2020 09:11:15: 11000000 INFO @ Tue, 16 Jun 2020 09:11:17: 2000000 INFO @ Tue, 16 Jun 2020 09:11:19: 7000000 INFO @ Tue, 16 Jun 2020 09:11:22: 12000000 INFO @ Tue, 16 Jun 2020 09:11:24: 3000000 INFO @ Tue, 16 Jun 2020 09:11:26: 8000000 INFO @ Tue, 16 Jun 2020 09:11:28: 13000000 INFO @ Tue, 16 Jun 2020 09:11:30: 4000000 INFO @ Tue, 16 Jun 2020 09:11:33: 9000000 INFO @ Tue, 16 Jun 2020 09:11:35: 14000000 INFO @ Tue, 16 Jun 2020 09:11:36: 5000000 INFO @ Tue, 16 Jun 2020 09:11:38: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:11:38: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:11:38: #1 total tags in treatment: 5693300 INFO @ Tue, 16 Jun 2020 09:11:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:11:38: #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 09:11:38: #1 tags after filtering in treatment: 5337456 INFO @ Tue, 16 Jun 2020 09:11:38: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 16 Jun 2020 09:11:38: #1 finished! INFO @ Tue, 16 Jun 2020 09:11:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:11:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:11:39: #2 number of paired peaks: 286 WARNING @ Tue, 16 Jun 2020 09:11:39: Fewer paired peaks (286) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 286 pairs to build model! INFO @ Tue, 16 Jun 2020 09:11:39: start model_add_line... INFO @ Tue, 16 Jun 2020 09:11:39: start X-correlation... INFO @ Tue, 16 Jun 2020 09:11:39: end of X-cor INFO @ Tue, 16 Jun 2020 09:11:39: #2 finished! INFO @ Tue, 16 Jun 2020 09:11:39: #2 predicted fragment length is 134 bps INFO @ Tue, 16 Jun 2020 09:11:39: #2 alternative fragment length(s) may be 4,93,134 bps INFO @ Tue, 16 Jun 2020 09:11:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085373/SRX4085373.05_model.r INFO @ Tue, 16 Jun 2020 09:11:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:11:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:11:39: 10000000 INFO @ Tue, 16 Jun 2020 09:11:43: 6000000 INFO @ Tue, 16 Jun 2020 09:11:45: 11000000 INFO @ Tue, 16 Jun 2020 09:11:49: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:11:49: 7000000 INFO @ Tue, 16 Jun 2020 09:11:52: 12000000 INFO @ Tue, 16 Jun 2020 09:11:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085373/SRX4085373.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:11:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085373/SRX4085373.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:11:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085373/SRX4085373.05_summits.bed INFO @ Tue, 16 Jun 2020 09:11:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (253 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:11:55: 8000000 INFO @ Tue, 16 Jun 2020 09:11:58: 13000000 INFO @ Tue, 16 Jun 2020 09:12:02: 9000000 INFO @ Tue, 16 Jun 2020 09:12:04: 14000000 INFO @ Tue, 16 Jun 2020 09:12:07: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:12:07: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:12:07: #1 total tags in treatment: 5693300 INFO @ Tue, 16 Jun 2020 09:12:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:07: #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 09:12:08: #1 tags after filtering in treatment: 5337456 INFO @ Tue, 16 Jun 2020 09:12:08: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 16 Jun 2020 09:12:08: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:08: #2 number of paired peaks: 286 WARNING @ Tue, 16 Jun 2020 09:12:08: Fewer paired peaks (286) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 286 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:08: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:08: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:08: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:08: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:08: #2 predicted fragment length is 134 bps INFO @ Tue, 16 Jun 2020 09:12:08: #2 alternative fragment length(s) may be 4,93,134 bps INFO @ Tue, 16 Jun 2020 09:12:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085373/SRX4085373.10_model.r INFO @ Tue, 16 Jun 2020 09:12:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:08: 10000000 INFO @ Tue, 16 Jun 2020 09:12:14: 11000000 INFO @ Tue, 16 Jun 2020 09:12:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:20: 12000000 INFO @ Tue, 16 Jun 2020 09:12:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085373/SRX4085373.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085373/SRX4085373.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085373/SRX4085373.10_summits.bed INFO @ Tue, 16 Jun 2020 09:12:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (179 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:12:26: 13000000 INFO @ Tue, 16 Jun 2020 09:12:32: 14000000 INFO @ Tue, 16 Jun 2020 09:12:35: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:12:35: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:12:35: #1 total tags in treatment: 5693300 INFO @ Tue, 16 Jun 2020 09:12:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:35: #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 09:12:35: #1 tags after filtering in treatment: 5337456 INFO @ Tue, 16 Jun 2020 09:12:35: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 16 Jun 2020 09:12:35: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:36: #2 number of paired peaks: 286 WARNING @ Tue, 16 Jun 2020 09:12:36: Fewer paired peaks (286) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 286 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:36: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:36: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:36: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:36: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:36: #2 predicted fragment length is 134 bps INFO @ Tue, 16 Jun 2020 09:12:36: #2 alternative fragment length(s) may be 4,93,134 bps INFO @ Tue, 16 Jun 2020 09:12:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085373/SRX4085373.20_model.r INFO @ Tue, 16 Jun 2020 09:12:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085373/SRX4085373.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085373/SRX4085373.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085373/SRX4085373.20_summits.bed INFO @ Tue, 16 Jun 2020 09:12:52: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (107 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。