Job ID = 6497384 SRX = SRX4085364 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T22:03:57 prefetch.2.10.7: 1) Downloading 'SRR7167393'... 2020-06-25T22:03:58 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:06:36 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:06:36 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: 00:10:41 13229488 reads; of these: 13229488 (100.00%) were paired; of these: 706505 (5.34%) aligned concordantly 0 times 10861499 (82.10%) aligned concordantly exactly 1 time 1661484 (12.56%) aligned concordantly >1 times ---- 706505 pairs aligned concordantly 0 times; of these: 207247 (29.33%) aligned discordantly 1 time ---- 499258 pairs aligned 0 times concordantly or discordantly; of these: 998516 mates make up the pairs; of these: 480985 (48.17%) aligned 0 times 370993 (37.15%) aligned exactly 1 time 146538 (14.68%) aligned >1 times 98.18% overall alignment rate Time searching: 00:10:41 Overall time: 00:10:41 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] 1202040 / 12593681 = 0.0954 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 07:26:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4085364/SRX4085364.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4085364/SRX4085364.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4085364/SRX4085364.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 07:26:07: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:26:07: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:26:13: 1000000 INFO @ Fri, 26 Jun 2020 07:26:18: 2000000 INFO @ Fri, 26 Jun 2020 07:26:23: 3000000 INFO @ Fri, 26 Jun 2020 07:26:28: 4000000 INFO @ Fri, 26 Jun 2020 07:26:33: 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 07:26:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4085364/SRX4085364.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4085364/SRX4085364.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4085364/SRX4085364.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 07:26:37: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:26:37: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:26:39: 6000000 INFO @ Fri, 26 Jun 2020 07:26:43: 1000000 INFO @ Fri, 26 Jun 2020 07:26:44: 7000000 INFO @ Fri, 26 Jun 2020 07:26:49: 2000000 INFO @ Fri, 26 Jun 2020 07:26:50: 8000000 INFO @ Fri, 26 Jun 2020 07:26:54: 3000000 INFO @ Fri, 26 Jun 2020 07:26:56: 9000000 INFO @ Fri, 26 Jun 2020 07:27:00: 4000000 INFO @ Fri, 26 Jun 2020 07:27:01: 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 07:27:06: 5000000 INFO @ Fri, 26 Jun 2020 07:27:07: 11000000 INFO @ Fri, 26 Jun 2020 07:27:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4085364/SRX4085364.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4085364/SRX4085364.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4085364/SRX4085364.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 07:27:07: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:27:07: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:27:12: 6000000 INFO @ Fri, 26 Jun 2020 07:27:13: 12000000 INFO @ Fri, 26 Jun 2020 07:27:13: 1000000 INFO @ Fri, 26 Jun 2020 07:27:18: 7000000 INFO @ Fri, 26 Jun 2020 07:27:18: 13000000 INFO @ Fri, 26 Jun 2020 07:27:19: 2000000 INFO @ Fri, 26 Jun 2020 07:27:24: 8000000 INFO @ Fri, 26 Jun 2020 07:27:24: 14000000 INFO @ Fri, 26 Jun 2020 07:27:25: 3000000 INFO @ Fri, 26 Jun 2020 07:27:29: 9000000 INFO @ Fri, 26 Jun 2020 07:27:30: 15000000 INFO @ Fri, 26 Jun 2020 07:27:30: 4000000 INFO @ Fri, 26 Jun 2020 07:27:35: 10000000 INFO @ Fri, 26 Jun 2020 07:27:36: 16000000 INFO @ Fri, 26 Jun 2020 07:27:36: 5000000 INFO @ Fri, 26 Jun 2020 07:27:41: 11000000 INFO @ Fri, 26 Jun 2020 07:27:41: 17000000 INFO @ Fri, 26 Jun 2020 07:27:43: 6000000 INFO @ Fri, 26 Jun 2020 07:27:46: 12000000 INFO @ Fri, 26 Jun 2020 07:27:47: 18000000 INFO @ Fri, 26 Jun 2020 07:27:49: 7000000 INFO @ Fri, 26 Jun 2020 07:27:52: 13000000 INFO @ Fri, 26 Jun 2020 07:27:52: 19000000 INFO @ Fri, 26 Jun 2020 07:27:55: 8000000 INFO @ Fri, 26 Jun 2020 07:27:57: 14000000 INFO @ Fri, 26 Jun 2020 07:27:58: 20000000 INFO @ Fri, 26 Jun 2020 07:28:01: 9000000 INFO @ Fri, 26 Jun 2020 07:28:03: 15000000 INFO @ Fri, 26 Jun 2020 07:28:03: 21000000 INFO @ Fri, 26 Jun 2020 07:28:06: 10000000 INFO @ Fri, 26 Jun 2020 07:28:09: 16000000 INFO @ Fri, 26 Jun 2020 07:28:09: 22000000 INFO @ Fri, 26 Jun 2020 07:28:12: 11000000 INFO @ Fri, 26 Jun 2020 07:28:14: 17000000 INFO @ Fri, 26 Jun 2020 07:28:14: 23000000 INFO @ Fri, 26 Jun 2020 07:28:17: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 07:28:17: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 07:28:17: #1 total tags in treatment: 11325958 INFO @ Fri, 26 Jun 2020 07:28:17: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:28:17: #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 07:28:17: 12000000 INFO @ Fri, 26 Jun 2020 07:28:18: #1 tags after filtering in treatment: 10350063 INFO @ Fri, 26 Jun 2020 07:28:18: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 26 Jun 2020 07:28:18: #1 finished! INFO @ Fri, 26 Jun 2020 07:28:18: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:28:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:28:18: #2 number of paired peaks: 189 WARNING @ Fri, 26 Jun 2020 07:28:18: Fewer paired peaks (189) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 189 pairs to build model! INFO @ Fri, 26 Jun 2020 07:28:18: start model_add_line... INFO @ Fri, 26 Jun 2020 07:28:18: start X-correlation... INFO @ Fri, 26 Jun 2020 07:28:18: end of X-cor INFO @ Fri, 26 Jun 2020 07:28:18: #2 finished! INFO @ Fri, 26 Jun 2020 07:28:18: #2 predicted fragment length is 155 bps INFO @ Fri, 26 Jun 2020 07:28:18: #2 alternative fragment length(s) may be 4,130,155 bps INFO @ Fri, 26 Jun 2020 07:28:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4085364/SRX4085364.05_model.r INFO @ Fri, 26 Jun 2020 07:28:18: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:28:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:28:19: 18000000 INFO @ Fri, 26 Jun 2020 07:28:23: 13000000 INFO @ Fri, 26 Jun 2020 07:28:25: 19000000 INFO @ Fri, 26 Jun 2020 07:28:29: 14000000 INFO @ Fri, 26 Jun 2020 07:28:30: 20000000 INFO @ Fri, 26 Jun 2020 07:28:34: 15000000 INFO @ Fri, 26 Jun 2020 07:28:36: 21000000 INFO @ Fri, 26 Jun 2020 07:28:38: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:28:40: 16000000 INFO @ Fri, 26 Jun 2020 07:28:41: 22000000 INFO @ Fri, 26 Jun 2020 07:28:45: 17000000 INFO @ Fri, 26 Jun 2020 07:28:46: 23000000 INFO @ Fri, 26 Jun 2020 07:28:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4085364/SRX4085364.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:28:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4085364/SRX4085364.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:28:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4085364/SRX4085364.05_summits.bed INFO @ Fri, 26 Jun 2020 07:28:48: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (261 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 INFO @ Fri, 26 Jun 2020 07:28:49: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 07:28:49: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 07:28:49: #1 total tags in treatment: 11325958 INFO @ Fri, 26 Jun 2020 07:28:49: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:28:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:28:50: #1 tags after filtering in treatment: 10350063 INFO @ Fri, 26 Jun 2020 07:28:50: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 26 Jun 2020 07:28:50: #1 finished! INFO @ Fri, 26 Jun 2020 07:28:50: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:28:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:28:50: #2 number of paired peaks: 189 WARNING @ Fri, 26 Jun 2020 07:28:50: Fewer paired peaks (189) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 189 pairs to build model! INFO @ Fri, 26 Jun 2020 07:28:50: start model_add_line... INFO @ Fri, 26 Jun 2020 07:28:50: start X-correlation... INFO @ Fri, 26 Jun 2020 07:28:50: end of X-cor INFO @ Fri, 26 Jun 2020 07:28:50: #2 finished! INFO @ Fri, 26 Jun 2020 07:28:50: #2 predicted fragment length is 155 bps INFO @ Fri, 26 Jun 2020 07:28:50: #2 alternative fragment length(s) may be 4,130,155 bps INFO @ Fri, 26 Jun 2020 07:28:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4085364/SRX4085364.10_model.r INFO @ Fri, 26 Jun 2020 07:28:50: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:28:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:28:51: 18000000 INFO @ Fri, 26 Jun 2020 07:28:56: 19000000 INFO @ Fri, 26 Jun 2020 07:29:01: 20000000 INFO @ Fri, 26 Jun 2020 07:29:06: 21000000 INFO @ Fri, 26 Jun 2020 07:29:11: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:29:11: 22000000 INFO @ Fri, 26 Jun 2020 07:29:16: 23000000 INFO @ Fri, 26 Jun 2020 07:29:19: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 07:29:19: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 07:29:19: #1 total tags in treatment: 11325958 INFO @ Fri, 26 Jun 2020 07:29:19: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:29:19: #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 07:29:19: #1 tags after filtering in treatment: 10350063 INFO @ Fri, 26 Jun 2020 07:29:19: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 26 Jun 2020 07:29:19: #1 finished! INFO @ Fri, 26 Jun 2020 07:29:19: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:29:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:29:20: #2 number of paired peaks: 189 WARNING @ Fri, 26 Jun 2020 07:29:20: Fewer paired peaks (189) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 189 pairs to build model! INFO @ Fri, 26 Jun 2020 07:29:20: start model_add_line... INFO @ Fri, 26 Jun 2020 07:29:20: start X-correlation... INFO @ Fri, 26 Jun 2020 07:29:20: end of X-cor INFO @ Fri, 26 Jun 2020 07:29:20: #2 finished! INFO @ Fri, 26 Jun 2020 07:29:20: #2 predicted fragment length is 155 bps INFO @ Fri, 26 Jun 2020 07:29:20: #2 alternative fragment length(s) may be 4,130,155 bps INFO @ Fri, 26 Jun 2020 07:29:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4085364/SRX4085364.20_model.r INFO @ Fri, 26 Jun 2020 07:29:20: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:29:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:29:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4085364/SRX4085364.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:29:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4085364/SRX4085364.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:29:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4085364/SRX4085364.10_summits.bed INFO @ Fri, 26 Jun 2020 07:29:20: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (200 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:29:40: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:29:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4085364/SRX4085364.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:29:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4085364/SRX4085364.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:29:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4085364/SRX4085364.20_summits.bed INFO @ Fri, 26 Jun 2020 07:29:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (125 records, 4 fields): 1 millis CompletedMACS2peakCalling