Job ID = 6367781 SRX = SRX4085351 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:39:44 prefetch.2.10.7: 1) Downloading 'SRR7167380'... 2020-06-15T23:39:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:49:01 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:49:01 prefetch.2.10.7: 1) 'SRR7167380' was downloaded successfully Read 21977351 spots for SRR7167380/SRR7167380.sra Written 21977351 spots for SRR7167380/SRR7167380.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: 00:16:07 21977351 reads; of these: 21977351 (100.00%) were paired; of these: 5777352 (26.29%) aligned concordantly 0 times 14130399 (64.30%) aligned concordantly exactly 1 time 2069600 (9.42%) aligned concordantly >1 times ---- 5777352 pairs aligned concordantly 0 times; of these: 444429 (7.69%) aligned discordantly 1 time ---- 5332923 pairs aligned 0 times concordantly or discordantly; of these: 10665846 mates make up the pairs; of these: 6900669 (64.70%) aligned 0 times 3162014 (29.65%) aligned exactly 1 time 603163 (5.66%) aligned >1 times 84.30% overall alignment rate Time searching: 00:16:07 Overall time: 00:16:07 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 16 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] 8158856 / 16300220 = 0.5005 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 09:17:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085351/SRX4085351.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085351/SRX4085351.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085351/SRX4085351.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085351/SRX4085351.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 09:17:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:17:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:17:25: 1000000 INFO @ Tue, 16 Jun 2020 09:17:31: 2000000 INFO @ Tue, 16 Jun 2020 09:17:38: 3000000 INFO @ Tue, 16 Jun 2020 09:17:44: 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 09:17:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085351/SRX4085351.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085351/SRX4085351.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085351/SRX4085351.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085351/SRX4085351.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 09:17:48: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:17:48: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:17:50: 5000000 INFO @ Tue, 16 Jun 2020 09:17:55: 1000000 INFO @ Tue, 16 Jun 2020 09:17:57: 6000000 INFO @ Tue, 16 Jun 2020 09:18:02: 2000000 INFO @ Tue, 16 Jun 2020 09:18:03: 7000000 INFO @ Tue, 16 Jun 2020 09:18:09: 3000000 INFO @ Tue, 16 Jun 2020 09:18:10: 8000000 INFO @ Tue, 16 Jun 2020 09:18:15: 4000000 INFO @ Tue, 16 Jun 2020 09:18:16: 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 09:18:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085351/SRX4085351.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085351/SRX4085351.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085351/SRX4085351.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085351/SRX4085351.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 09:18:18: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:18:18: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:18:22: 5000000 INFO @ Tue, 16 Jun 2020 09:18:23: 10000000 INFO @ Tue, 16 Jun 2020 09:18:24: 1000000 INFO @ Tue, 16 Jun 2020 09:18:28: 6000000 INFO @ Tue, 16 Jun 2020 09:18:29: 11000000 INFO @ Tue, 16 Jun 2020 09:18:30: 2000000 INFO @ Tue, 16 Jun 2020 09:18:35: 7000000 INFO @ Tue, 16 Jun 2020 09:18:36: 3000000 INFO @ Tue, 16 Jun 2020 09:18:36: 12000000 INFO @ Tue, 16 Jun 2020 09:18:42: 8000000 INFO @ Tue, 16 Jun 2020 09:18:42: 4000000 INFO @ Tue, 16 Jun 2020 09:18:42: 13000000 INFO @ Tue, 16 Jun 2020 09:18:48: 5000000 INFO @ Tue, 16 Jun 2020 09:18:48: 9000000 INFO @ Tue, 16 Jun 2020 09:18:49: 14000000 INFO @ Tue, 16 Jun 2020 09:18:54: 6000000 INFO @ Tue, 16 Jun 2020 09:18:55: 10000000 INFO @ Tue, 16 Jun 2020 09:18:56: 15000000 INFO @ Tue, 16 Jun 2020 09:18:59: 7000000 INFO @ Tue, 16 Jun 2020 09:19:02: 11000000 INFO @ Tue, 16 Jun 2020 09:19:03: 16000000 INFO @ Tue, 16 Jun 2020 09:19:05: 8000000 INFO @ Tue, 16 Jun 2020 09:19:09: 12000000 INFO @ Tue, 16 Jun 2020 09:19:10: 17000000 INFO @ Tue, 16 Jun 2020 09:19:11: 9000000 INFO @ Tue, 16 Jun 2020 09:19:16: 13000000 INFO @ Tue, 16 Jun 2020 09:19:17: 18000000 INFO @ Tue, 16 Jun 2020 09:19:17: 10000000 INFO @ Tue, 16 Jun 2020 09:19:22: 14000000 INFO @ Tue, 16 Jun 2020 09:19:23: 11000000 INFO @ Tue, 16 Jun 2020 09:19:23: 19000000 INFO @ Tue, 16 Jun 2020 09:19:29: 12000000 INFO @ Tue, 16 Jun 2020 09:19:29: 15000000 INFO @ Tue, 16 Jun 2020 09:19:30: 20000000 INFO @ Tue, 16 Jun 2020 09:19:34: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:19:34: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:19:34: #1 total tags in treatment: 8085720 INFO @ Tue, 16 Jun 2020 09:19:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:19:34: #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 09:19:35: #1 tags after filtering in treatment: 6868902 INFO @ Tue, 16 Jun 2020 09:19:35: #1 Redundant rate of treatment: 0.15 INFO @ Tue, 16 Jun 2020 09:19:35: #1 finished! INFO @ Tue, 16 Jun 2020 09:19:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:19:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:19:35: 13000000 INFO @ Tue, 16 Jun 2020 09:19:35: #2 number of paired peaks: 546 WARNING @ Tue, 16 Jun 2020 09:19:35: Fewer paired peaks (546) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 546 pairs to build model! INFO @ Tue, 16 Jun 2020 09:19:35: start model_add_line... INFO @ Tue, 16 Jun 2020 09:19:35: start X-correlation... INFO @ Tue, 16 Jun 2020 09:19:35: end of X-cor INFO @ Tue, 16 Jun 2020 09:19:35: #2 finished! INFO @ Tue, 16 Jun 2020 09:19:35: #2 predicted fragment length is 112 bps INFO @ Tue, 16 Jun 2020 09:19:35: #2 alternative fragment length(s) may be 112 bps INFO @ Tue, 16 Jun 2020 09:19:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085351/SRX4085351.05_model.r INFO @ Tue, 16 Jun 2020 09:19:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:19:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:19:36: 16000000 INFO @ Tue, 16 Jun 2020 09:19:41: 14000000 INFO @ Tue, 16 Jun 2020 09:19:43: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:19:46: 15000000 INFO @ Tue, 16 Jun 2020 09:19:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:19:50: 18000000 INFO @ Tue, 16 Jun 2020 09:19:52: 16000000 INFO @ Tue, 16 Jun 2020 09:19:57: 19000000 INFO @ Tue, 16 Jun 2020 09:19:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085351/SRX4085351.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:19:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085351/SRX4085351.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:19:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085351/SRX4085351.05_summits.bed INFO @ Tue, 16 Jun 2020 09:19:58: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (2254 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:19:58: 17000000 INFO @ Tue, 16 Jun 2020 09:20:03: 20000000 INFO @ Tue, 16 Jun 2020 09:20:04: 18000000 INFO @ Tue, 16 Jun 2020 09:20:08: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:20:08: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:20:08: #1 total tags in treatment: 8085720 INFO @ Tue, 16 Jun 2020 09:20:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:20:08: #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 09:20:08: #1 tags after filtering in treatment: 6868902 INFO @ Tue, 16 Jun 2020 09:20:08: #1 Redundant rate of treatment: 0.15 INFO @ Tue, 16 Jun 2020 09:20:08: #1 finished! INFO @ Tue, 16 Jun 2020 09:20:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:20:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:20:09: #2 number of paired peaks: 546 WARNING @ Tue, 16 Jun 2020 09:20:09: Fewer paired peaks (546) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 546 pairs to build model! INFO @ Tue, 16 Jun 2020 09:20:09: start model_add_line... INFO @ Tue, 16 Jun 2020 09:20:09: start X-correlation... INFO @ Tue, 16 Jun 2020 09:20:09: end of X-cor INFO @ Tue, 16 Jun 2020 09:20:09: #2 finished! INFO @ Tue, 16 Jun 2020 09:20:09: #2 predicted fragment length is 112 bps INFO @ Tue, 16 Jun 2020 09:20:09: #2 alternative fragment length(s) may be 112 bps INFO @ Tue, 16 Jun 2020 09:20:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085351/SRX4085351.10_model.r INFO @ Tue, 16 Jun 2020 09:20:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:20:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:20:10: 19000000 INFO @ Tue, 16 Jun 2020 09:20:15: 20000000 INFO @ Tue, 16 Jun 2020 09:20:19: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:20:19: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:20:19: #1 total tags in treatment: 8085720 INFO @ Tue, 16 Jun 2020 09:20:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:20:19: #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 09:20:19: #1 tags after filtering in treatment: 6868902 INFO @ Tue, 16 Jun 2020 09:20:19: #1 Redundant rate of treatment: 0.15 INFO @ Tue, 16 Jun 2020 09:20:19: #1 finished! INFO @ Tue, 16 Jun 2020 09:20:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:20:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:20:20: #2 number of paired peaks: 546 WARNING @ Tue, 16 Jun 2020 09:20:20: Fewer paired peaks (546) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 546 pairs to build model! INFO @ Tue, 16 Jun 2020 09:20:20: start model_add_line... INFO @ Tue, 16 Jun 2020 09:20:20: start X-correlation... INFO @ Tue, 16 Jun 2020 09:20:20: end of X-cor INFO @ Tue, 16 Jun 2020 09:20:20: #2 finished! INFO @ Tue, 16 Jun 2020 09:20:20: #2 predicted fragment length is 112 bps INFO @ Tue, 16 Jun 2020 09:20:20: #2 alternative fragment length(s) may be 112 bps INFO @ Tue, 16 Jun 2020 09:20:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085351/SRX4085351.20_model.r INFO @ Tue, 16 Jun 2020 09:20:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:20:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:20:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:20:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085351/SRX4085351.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:20:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085351/SRX4085351.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:20:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085351/SRX4085351.10_summits.bed INFO @ Tue, 16 Jun 2020 09:20:31: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1456 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:20:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:20:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085351/SRX4085351.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:20:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085351/SRX4085351.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:20:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085351/SRX4085351.20_summits.bed INFO @ Tue, 16 Jun 2020 09:20:42: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (787 records, 4 fields): 4 millis CompletedMACS2peakCalling