Job ID = 6367202 SRX = SRX2978706 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:24:31 prefetch.2.10.7: 1) Downloading 'SRR5799213'... 2020-06-15T23:24:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:27:19 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:27:19 prefetch.2.10.7: 1) 'SRR5799213' was downloaded successfully 2020-06-15T23:27:19 prefetch.2.10.7: 'SRR5799213' has 0 unresolved dependencies Read 21146525 spots for SRR5799213/SRR5799213.sra Written 21146525 spots for SRR5799213/SRR5799213.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: 00:18:14 21146525 reads; of these: 21146525 (100.00%) were paired; of these: 1215522 (5.75%) aligned concordantly 0 times 17135725 (81.03%) aligned concordantly exactly 1 time 2795278 (13.22%) aligned concordantly >1 times ---- 1215522 pairs aligned concordantly 0 times; of these: 690523 (56.81%) aligned discordantly 1 time ---- 524999 pairs aligned 0 times concordantly or discordantly; of these: 1049998 mates make up the pairs; of these: 606563 (57.77%) aligned 0 times 261550 (24.91%) aligned exactly 1 time 181885 (17.32%) aligned >1 times 98.57% overall alignment rate Time searching: 00:18:14 Overall time: 00:18:14 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] 355281 / 20611031 = 0.0172 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 08:58:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2978706/SRX2978706.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2978706/SRX2978706.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2978706/SRX2978706.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2978706/SRX2978706.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 08:58:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:58:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:58:48: 1000000 INFO @ Tue, 16 Jun 2020 08:58:54: 2000000 INFO @ Tue, 16 Jun 2020 08:59:01: 3000000 INFO @ Tue, 16 Jun 2020 08:59:07: 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 08:59:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2978706/SRX2978706.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2978706/SRX2978706.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2978706/SRX2978706.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2978706/SRX2978706.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 08:59:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:59:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:59:14: 5000000 INFO @ Tue, 16 Jun 2020 08:59:18: 1000000 INFO @ Tue, 16 Jun 2020 08:59:20: 6000000 INFO @ Tue, 16 Jun 2020 08:59:24: 2000000 INFO @ Tue, 16 Jun 2020 08:59:28: 7000000 INFO @ Tue, 16 Jun 2020 08:59:30: 3000000 INFO @ Tue, 16 Jun 2020 08:59:35: 8000000 INFO @ Tue, 16 Jun 2020 08:59:36: 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 08:59:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2978706/SRX2978706.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2978706/SRX2978706.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2978706/SRX2978706.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2978706/SRX2978706.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 08:59:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:59:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:59:42: 9000000 INFO @ Tue, 16 Jun 2020 08:59:42: 5000000 INFO @ Tue, 16 Jun 2020 08:59:48: 1000000 INFO @ Tue, 16 Jun 2020 08:59:48: 6000000 INFO @ Tue, 16 Jun 2020 08:59:49: 10000000 INFO @ Tue, 16 Jun 2020 08:59:54: 2000000 INFO @ Tue, 16 Jun 2020 08:59:55: 7000000 INFO @ Tue, 16 Jun 2020 08:59:56: 11000000 INFO @ Tue, 16 Jun 2020 09:00:00: 3000000 INFO @ Tue, 16 Jun 2020 09:00:01: 8000000 INFO @ Tue, 16 Jun 2020 09:00:03: 12000000 INFO @ Tue, 16 Jun 2020 09:00:07: 4000000 INFO @ Tue, 16 Jun 2020 09:00:07: 9000000 INFO @ Tue, 16 Jun 2020 09:00:11: 13000000 INFO @ Tue, 16 Jun 2020 09:00:13: 5000000 INFO @ Tue, 16 Jun 2020 09:00:13: 10000000 INFO @ Tue, 16 Jun 2020 09:00:18: 14000000 INFO @ Tue, 16 Jun 2020 09:00:19: 6000000 INFO @ Tue, 16 Jun 2020 09:00:20: 11000000 INFO @ Tue, 16 Jun 2020 09:00:25: 15000000 INFO @ Tue, 16 Jun 2020 09:00:26: 7000000 INFO @ Tue, 16 Jun 2020 09:00:26: 12000000 INFO @ Tue, 16 Jun 2020 09:00:32: 8000000 INFO @ Tue, 16 Jun 2020 09:00:33: 13000000 INFO @ Tue, 16 Jun 2020 09:00:33: 16000000 INFO @ Tue, 16 Jun 2020 09:00:38: 9000000 INFO @ Tue, 16 Jun 2020 09:00:39: 14000000 INFO @ Tue, 16 Jun 2020 09:00:40: 17000000 INFO @ Tue, 16 Jun 2020 09:00:45: 10000000 INFO @ Tue, 16 Jun 2020 09:00:45: 15000000 INFO @ Tue, 16 Jun 2020 09:00:48: 18000000 INFO @ Tue, 16 Jun 2020 09:00:51: 11000000 INFO @ Tue, 16 Jun 2020 09:00:52: 16000000 INFO @ Tue, 16 Jun 2020 09:00:55: 19000000 INFO @ Tue, 16 Jun 2020 09:00:58: 12000000 INFO @ Tue, 16 Jun 2020 09:00:58: 17000000 INFO @ Tue, 16 Jun 2020 09:01:03: 20000000 INFO @ Tue, 16 Jun 2020 09:01:04: 13000000 INFO @ Tue, 16 Jun 2020 09:01:05: 18000000 INFO @ Tue, 16 Jun 2020 09:01:10: 21000000 INFO @ Tue, 16 Jun 2020 09:01:11: 14000000 INFO @ Tue, 16 Jun 2020 09:01:11: 19000000 INFO @ Tue, 16 Jun 2020 09:01:17: 15000000 INFO @ Tue, 16 Jun 2020 09:01:17: 20000000 INFO @ Tue, 16 Jun 2020 09:01:18: 22000000 INFO @ Tue, 16 Jun 2020 09:01:24: 16000000 INFO @ Tue, 16 Jun 2020 09:01:24: 21000000 INFO @ Tue, 16 Jun 2020 09:01:25: 23000000 INFO @ Tue, 16 Jun 2020 09:01:31: 17000000 INFO @ Tue, 16 Jun 2020 09:01:31: 22000000 INFO @ Tue, 16 Jun 2020 09:01:33: 24000000 INFO @ Tue, 16 Jun 2020 09:01:37: 18000000 INFO @ Tue, 16 Jun 2020 09:01:38: 23000000 INFO @ Tue, 16 Jun 2020 09:01:40: 25000000 INFO @ Tue, 16 Jun 2020 09:01:44: 19000000 INFO @ Tue, 16 Jun 2020 09:01:44: 24000000 INFO @ Tue, 16 Jun 2020 09:01:48: 26000000 INFO @ Tue, 16 Jun 2020 09:01:50: 20000000 INFO @ Tue, 16 Jun 2020 09:01:51: 25000000 INFO @ Tue, 16 Jun 2020 09:01:55: 27000000 INFO @ Tue, 16 Jun 2020 09:01:56: 21000000 INFO @ Tue, 16 Jun 2020 09:01:58: 26000000 INFO @ Tue, 16 Jun 2020 09:02:03: 28000000 INFO @ Tue, 16 Jun 2020 09:02:03: 22000000 INFO @ Tue, 16 Jun 2020 09:02:04: 27000000 INFO @ Tue, 16 Jun 2020 09:02:09: 23000000 INFO @ Tue, 16 Jun 2020 09:02:10: 29000000 INFO @ Tue, 16 Jun 2020 09:02:11: 28000000 INFO @ Tue, 16 Jun 2020 09:02:16: 24000000 INFO @ Tue, 16 Jun 2020 09:02:17: 30000000 INFO @ Tue, 16 Jun 2020 09:02:17: 29000000 INFO @ Tue, 16 Jun 2020 09:02:22: 25000000 INFO @ Tue, 16 Jun 2020 09:02:24: 30000000 INFO @ Tue, 16 Jun 2020 09:02:24: 31000000 INFO @ Tue, 16 Jun 2020 09:02:28: 26000000 INFO @ Tue, 16 Jun 2020 09:02:30: 31000000 INFO @ Tue, 16 Jun 2020 09:02:31: 32000000 INFO @ Tue, 16 Jun 2020 09:02:35: 27000000 INFO @ Tue, 16 Jun 2020 09:02:37: 32000000 INFO @ Tue, 16 Jun 2020 09:02:39: 33000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:02:41: 28000000 INFO @ Tue, 16 Jun 2020 09:02:44: 33000000 INFO @ Tue, 16 Jun 2020 09:02:46: 34000000 INFO @ Tue, 16 Jun 2020 09:02:48: 29000000 INFO @ Tue, 16 Jun 2020 09:02:50: 34000000 INFO @ Tue, 16 Jun 2020 09:02:53: 35000000 INFO @ Tue, 16 Jun 2020 09:02:54: 30000000 INFO @ Tue, 16 Jun 2020 09:02:57: 35000000 INFO @ Tue, 16 Jun 2020 09:03:00: 31000000 INFO @ Tue, 16 Jun 2020 09:03:00: 36000000 INFO @ Tue, 16 Jun 2020 09:03:03: 36000000 INFO @ Tue, 16 Jun 2020 09:03:07: 32000000 INFO @ Tue, 16 Jun 2020 09:03:07: 37000000 INFO @ Tue, 16 Jun 2020 09:03:10: 37000000 INFO @ Tue, 16 Jun 2020 09:03:13: 33000000 INFO @ Tue, 16 Jun 2020 09:03:15: 38000000 INFO @ Tue, 16 Jun 2020 09:03:16: 38000000 INFO @ Tue, 16 Jun 2020 09:03:20: 34000000 INFO @ Tue, 16 Jun 2020 09:03:22: 39000000 INFO @ Tue, 16 Jun 2020 09:03:23: 39000000 INFO @ Tue, 16 Jun 2020 09:03:26: 35000000 INFO @ Tue, 16 Jun 2020 09:03:29: 40000000 INFO @ Tue, 16 Jun 2020 09:03:29: 40000000 INFO @ Tue, 16 Jun 2020 09:03:33: 36000000 INFO @ Tue, 16 Jun 2020 09:03:36: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:03:36: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:03:36: #1 total tags in treatment: 19580003 INFO @ Tue, 16 Jun 2020 09:03:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:03:36: #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 09:03:36: #1 tags after filtering in treatment: 17554632 INFO @ Tue, 16 Jun 2020 09:03:36: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 16 Jun 2020 09:03:36: #1 finished! INFO @ Tue, 16 Jun 2020 09:03:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:03:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:03:36: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:03:36: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:03:36: #1 total tags in treatment: 19580003 INFO @ Tue, 16 Jun 2020 09:03:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:03:36: #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 09:03:37: #1 tags after filtering in treatment: 17554632 INFO @ Tue, 16 Jun 2020 09:03:37: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 16 Jun 2020 09:03:37: #1 finished! INFO @ Tue, 16 Jun 2020 09:03:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:03:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:03:37: #2 number of paired peaks: 284 WARNING @ Tue, 16 Jun 2020 09:03:37: Fewer paired peaks (284) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 284 pairs to build model! INFO @ Tue, 16 Jun 2020 09:03:37: start model_add_line... INFO @ Tue, 16 Jun 2020 09:03:38: start X-correlation... INFO @ Tue, 16 Jun 2020 09:03:38: end of X-cor INFO @ Tue, 16 Jun 2020 09:03:38: #2 finished! INFO @ Tue, 16 Jun 2020 09:03:38: #2 predicted fragment length is 112 bps INFO @ Tue, 16 Jun 2020 09:03:38: #2 alternative fragment length(s) may be 4,112,132 bps INFO @ Tue, 16 Jun 2020 09:03:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2978706/SRX2978706.05_model.r INFO @ Tue, 16 Jun 2020 09:03:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:03:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:03:38: #2 number of paired peaks: 284 WARNING @ Tue, 16 Jun 2020 09:03:38: Fewer paired peaks (284) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 284 pairs to build model! INFO @ Tue, 16 Jun 2020 09:03:38: start model_add_line... INFO @ Tue, 16 Jun 2020 09:03:38: start X-correlation... INFO @ Tue, 16 Jun 2020 09:03:38: end of X-cor INFO @ Tue, 16 Jun 2020 09:03:38: #2 finished! INFO @ Tue, 16 Jun 2020 09:03:38: #2 predicted fragment length is 112 bps INFO @ Tue, 16 Jun 2020 09:03:38: #2 alternative fragment length(s) may be 4,112,132 bps INFO @ Tue, 16 Jun 2020 09:03:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2978706/SRX2978706.10_model.r INFO @ Tue, 16 Jun 2020 09:03:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:03:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:03:39: 37000000 INFO @ Tue, 16 Jun 2020 09:03:44: 38000000 INFO @ Tue, 16 Jun 2020 09:03:50: 39000000 INFO @ Tue, 16 Jun 2020 09:03:55: 40000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:04:00: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:04:00: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:04:00: #1 total tags in treatment: 19580003 INFO @ Tue, 16 Jun 2020 09:04:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:04:00: #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 09:04:01: #1 tags after filtering in treatment: 17554632 INFO @ Tue, 16 Jun 2020 09:04:01: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 16 Jun 2020 09:04:01: #1 finished! INFO @ Tue, 16 Jun 2020 09:04:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:04:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:04:02: #2 number of paired peaks: 284 WARNING @ Tue, 16 Jun 2020 09:04:02: Fewer paired peaks (284) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 284 pairs to build model! INFO @ Tue, 16 Jun 2020 09:04:02: start model_add_line... INFO @ Tue, 16 Jun 2020 09:04:02: start X-correlation... INFO @ Tue, 16 Jun 2020 09:04:02: end of X-cor INFO @ Tue, 16 Jun 2020 09:04:02: #2 finished! INFO @ Tue, 16 Jun 2020 09:04:02: #2 predicted fragment length is 112 bps INFO @ Tue, 16 Jun 2020 09:04:02: #2 alternative fragment length(s) may be 4,112,132 bps INFO @ Tue, 16 Jun 2020 09:04:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2978706/SRX2978706.20_model.r INFO @ Tue, 16 Jun 2020 09:04:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:04:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:04:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:04:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:04:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2978706/SRX2978706.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:04:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2978706/SRX2978706.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:04:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2978706/SRX2978706.05_summits.bed INFO @ Tue, 16 Jun 2020 09:04:30: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (494 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:04:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2978706/SRX2978706.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:04:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2978706/SRX2978706.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:04:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2978706/SRX2978706.10_summits.bed INFO @ Tue, 16 Jun 2020 09:04:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (376 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:04:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:04:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2978706/SRX2978706.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:04:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2978706/SRX2978706.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:04:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2978706/SRX2978706.20_summits.bed INFO @ Tue, 16 Jun 2020 09:04:54: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (235 records, 4 fields): 2 millis CompletedMACS2peakCalling