Job ID = 6507773 SRX = SRX4085364 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T13:27:34 prefetch.2.10.7: 1) Downloading 'SRR7167393'... 2020-06-26T13:27:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:34:27 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:34:27 prefetch.2.10.7: 1) 'SRR7167393' was downloaded successfully Read 13229488 spots for SRR7167393/SRR7167393.sra Written 13229488 spots for SRR7167393/SRR7167393.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: 00:12:54 13229488 reads; of these: 13229488 (100.00%) were paired; of these: 706320 (5.34%) aligned concordantly 0 times 10861549 (82.10%) aligned concordantly exactly 1 time 1661619 (12.56%) aligned concordantly >1 times ---- 706320 pairs aligned concordantly 0 times; of these: 207260 (29.34%) aligned discordantly 1 time ---- 499060 pairs aligned 0 times concordantly or discordantly; of these: 998120 mates make up the pairs; of these: 480626 (48.15%) aligned 0 times 370965 (37.17%) aligned exactly 1 time 146529 (14.68%) aligned >1 times 98.18% overall alignment rate Time searching: 00:12:55 Overall time: 00:12:55 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] 1202144 / 12593872 = 0.0955 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 @ Fri, 26 Jun 2020 22:57:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085364/SRX4085364.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085364/SRX4085364.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085364/SRX4085364.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085364/SRX4085364.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 @ Fri, 26 Jun 2020 22:57:47: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:57:47: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:57:53: 1000000 INFO @ Fri, 26 Jun 2020 22:57:58: 2000000 INFO @ Fri, 26 Jun 2020 22:58:04: 3000000 INFO @ Fri, 26 Jun 2020 22:58:09: 4000000 INFO @ Fri, 26 Jun 2020 22:58:14: 5000000 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 @ Fri, 26 Jun 2020 22:58:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085364/SRX4085364.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085364/SRX4085364.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085364/SRX4085364.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085364/SRX4085364.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 @ Fri, 26 Jun 2020 22:58:18: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:58:18: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:58:20: 6000000 INFO @ Fri, 26 Jun 2020 22:58:23: 1000000 INFO @ Fri, 26 Jun 2020 22:58:25: 7000000 INFO @ Fri, 26 Jun 2020 22:58:29: 2000000 INFO @ Fri, 26 Jun 2020 22:58:30: 8000000 INFO @ Fri, 26 Jun 2020 22:58:34: 3000000 INFO @ Fri, 26 Jun 2020 22:58:35: 9000000 INFO @ Fri, 26 Jun 2020 22:58:40: 4000000 INFO @ Fri, 26 Jun 2020 22:58:41: 10000000 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 @ Fri, 26 Jun 2020 22:58:45: 5000000 INFO @ Fri, 26 Jun 2020 22:58:46: 11000000 INFO @ Fri, 26 Jun 2020 22:58:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085364/SRX4085364.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085364/SRX4085364.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085364/SRX4085364.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085364/SRX4085364.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 @ Fri, 26 Jun 2020 22:58:48: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:58:48: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:58:51: 6000000 INFO @ Fri, 26 Jun 2020 22:58:52: 12000000 INFO @ Fri, 26 Jun 2020 22:58:54: 1000000 INFO @ Fri, 26 Jun 2020 22:58:56: 7000000 INFO @ Fri, 26 Jun 2020 22:58:58: 13000000 INFO @ Fri, 26 Jun 2020 22:58:59: 2000000 INFO @ Fri, 26 Jun 2020 22:59:02: 8000000 INFO @ Fri, 26 Jun 2020 22:59:03: 14000000 INFO @ Fri, 26 Jun 2020 22:59:05: 3000000 INFO @ Fri, 26 Jun 2020 22:59:08: 9000000 INFO @ Fri, 26 Jun 2020 22:59:09: 15000000 INFO @ Fri, 26 Jun 2020 22:59:11: 4000000 INFO @ Fri, 26 Jun 2020 22:59:13: 10000000 INFO @ Fri, 26 Jun 2020 22:59:15: 16000000 INFO @ Fri, 26 Jun 2020 22:59:17: 5000000 INFO @ Fri, 26 Jun 2020 22:59:19: 11000000 INFO @ Fri, 26 Jun 2020 22:59:21: 17000000 INFO @ Fri, 26 Jun 2020 22:59:23: 6000000 INFO @ Fri, 26 Jun 2020 22:59:24: 12000000 INFO @ Fri, 26 Jun 2020 22:59:27: 18000000 INFO @ Fri, 26 Jun 2020 22:59:29: 7000000 INFO @ Fri, 26 Jun 2020 22:59:30: 13000000 INFO @ Fri, 26 Jun 2020 22:59:33: 19000000 INFO @ Fri, 26 Jun 2020 22:59:35: 8000000 INFO @ Fri, 26 Jun 2020 22:59:36: 14000000 INFO @ Fri, 26 Jun 2020 22:59:39: 20000000 INFO @ Fri, 26 Jun 2020 22:59:41: 9000000 INFO @ Fri, 26 Jun 2020 22:59:41: 15000000 INFO @ Fri, 26 Jun 2020 22:59:45: 21000000 INFO @ Fri, 26 Jun 2020 22:59:47: 16000000 INFO @ Fri, 26 Jun 2020 22:59:47: 10000000 INFO @ Fri, 26 Jun 2020 22:59:50: 22000000 INFO @ Fri, 26 Jun 2020 22:59:52: 17000000 INFO @ Fri, 26 Jun 2020 22:59:53: 11000000 INFO @ Fri, 26 Jun 2020 22:59:56: 23000000 INFO @ Fri, 26 Jun 2020 22:59:58: 18000000 INFO @ Fri, 26 Jun 2020 22:59:59: 12000000 INFO @ Fri, 26 Jun 2020 23:00:00: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 23:00:00: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 23:00:00: #1 total tags in treatment: 11326041 INFO @ Fri, 26 Jun 2020 23:00:00: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:00:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:00:00: #1 tags after filtering in treatment: 10350141 INFO @ Fri, 26 Jun 2020 23:00:00: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 26 Jun 2020 23:00:00: #1 finished! INFO @ Fri, 26 Jun 2020 23:00:00: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:00:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:00:01: #2 number of paired peaks: 190 WARNING @ Fri, 26 Jun 2020 23:00:01: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Fri, 26 Jun 2020 23:00:01: start model_add_line... INFO @ Fri, 26 Jun 2020 23:00:01: start X-correlation... INFO @ Fri, 26 Jun 2020 23:00:01: end of X-cor INFO @ Fri, 26 Jun 2020 23:00:01: #2 finished! INFO @ Fri, 26 Jun 2020 23:00:01: #2 predicted fragment length is 131 bps INFO @ Fri, 26 Jun 2020 23:00:01: #2 alternative fragment length(s) may be 4,113,131,154 bps INFO @ Fri, 26 Jun 2020 23:00:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085364/SRX4085364.05_model.r INFO @ Fri, 26 Jun 2020 23:00:01: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:00:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:00:03: 19000000 INFO @ Fri, 26 Jun 2020 23:00:05: 13000000 INFO @ Fri, 26 Jun 2020 23:00:08: 20000000 INFO @ Fri, 26 Jun 2020 23:00:10: 14000000 INFO @ Fri, 26 Jun 2020 23:00:14: 21000000 INFO @ Fri, 26 Jun 2020 23:00:15: 15000000 INFO @ Fri, 26 Jun 2020 23:00:19: 22000000 INFO @ Fri, 26 Jun 2020 23:00:19: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:00:21: 16000000 INFO @ Fri, 26 Jun 2020 23:00:24: 23000000 INFO @ Fri, 26 Jun 2020 23:00:26: 17000000 INFO @ Fri, 26 Jun 2020 23:00:27: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 23:00:27: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 23:00:27: #1 total tags in treatment: 11326041 INFO @ Fri, 26 Jun 2020 23:00:27: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:00:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:00:28: #1 tags after filtering in treatment: 10350141 INFO @ Fri, 26 Jun 2020 23:00:28: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 26 Jun 2020 23:00:28: #1 finished! INFO @ Fri, 26 Jun 2020 23:00:28: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:00:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:00:28: #2 number of paired peaks: 190 WARNING @ Fri, 26 Jun 2020 23:00:28: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Fri, 26 Jun 2020 23:00:28: start model_add_line... INFO @ Fri, 26 Jun 2020 23:00:28: start X-correlation... INFO @ Fri, 26 Jun 2020 23:00:28: end of X-cor INFO @ Fri, 26 Jun 2020 23:00:28: #2 finished! INFO @ Fri, 26 Jun 2020 23:00:28: #2 predicted fragment length is 131 bps INFO @ Fri, 26 Jun 2020 23:00:28: #2 alternative fragment length(s) may be 4,113,131,154 bps INFO @ Fri, 26 Jun 2020 23:00:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085364/SRX4085364.10_model.r INFO @ Fri, 26 Jun 2020 23:00:28: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:00:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:00:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085364/SRX4085364.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:00:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085364/SRX4085364.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:00:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085364/SRX4085364.05_summits.bed INFO @ Fri, 26 Jun 2020 23:00:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (283 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:00:31: 18000000 INFO @ Fri, 26 Jun 2020 23:00:37: 19000000 INFO @ Fri, 26 Jun 2020 23:00:42: 20000000 INFO @ Fri, 26 Jun 2020 23:00:47: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:00:47: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:00:52: 22000000 INFO @ Fri, 26 Jun 2020 23:00:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085364/SRX4085364.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:00:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085364/SRX4085364.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:00:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085364/SRX4085364.10_summits.bed INFO @ Fri, 26 Jun 2020 23:00:56: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (210 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:00:58: 23000000 INFO @ Fri, 26 Jun 2020 23:01:01: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 23:01:01: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 23:01:01: #1 total tags in treatment: 11326041 INFO @ Fri, 26 Jun 2020 23:01:01: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:01:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:01:01: #1 tags after filtering in treatment: 10350141 INFO @ Fri, 26 Jun 2020 23:01:01: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 26 Jun 2020 23:01:01: #1 finished! INFO @ Fri, 26 Jun 2020 23:01:01: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:01:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:01:02: #2 number of paired peaks: 190 WARNING @ Fri, 26 Jun 2020 23:01:02: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Fri, 26 Jun 2020 23:01:02: start model_add_line... INFO @ Fri, 26 Jun 2020 23:01:02: start X-correlation... INFO @ Fri, 26 Jun 2020 23:01:02: end of X-cor INFO @ Fri, 26 Jun 2020 23:01:02: #2 finished! INFO @ Fri, 26 Jun 2020 23:01:02: #2 predicted fragment length is 131 bps INFO @ Fri, 26 Jun 2020 23:01:02: #2 alternative fragment length(s) may be 4,113,131,154 bps INFO @ Fri, 26 Jun 2020 23:01:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085364/SRX4085364.20_model.r INFO @ Fri, 26 Jun 2020 23:01:02: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:01:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:01:20: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:01:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085364/SRX4085364.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:01:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085364/SRX4085364.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:01:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085364/SRX4085364.20_summits.bed INFO @ Fri, 26 Jun 2020 23:01:30: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (133 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。