Job ID = 6367769 SRX = SRX4085339 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:41:29 prefetch.2.10.7: 1) Downloading 'SRR7167368'... 2020-06-15T23:41:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:52:24 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:52:24 prefetch.2.10.7: 1) 'SRR7167368' was downloaded successfully Read 26268412 spots for SRR7167368/SRR7167368.sra Written 26268412 spots for SRR7167368/SRR7167368.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: 00:20:08 26268412 reads; of these: 26268412 (100.00%) were paired; of these: 1947315 (7.41%) aligned concordantly 0 times 21625857 (82.33%) aligned concordantly exactly 1 time 2695240 (10.26%) aligned concordantly >1 times ---- 1947315 pairs aligned concordantly 0 times; of these: 155253 (7.97%) aligned discordantly 1 time ---- 1792062 pairs aligned 0 times concordantly or discordantly; of these: 3584124 mates make up the pairs; of these: 2411850 (67.29%) aligned 0 times 974655 (27.19%) aligned exactly 1 time 197619 (5.51%) aligned >1 times 95.41% overall alignment rate Time searching: 00:20:08 Overall time: 00:20:08 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 24 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] 10576781 / 24447676 = 0.4326 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 09:26:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085339/SRX4085339.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085339/SRX4085339.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085339/SRX4085339.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085339/SRX4085339.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 09:26:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:26:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:26:39: 1000000 INFO @ Tue, 16 Jun 2020 09:26:45: 2000000 INFO @ Tue, 16 Jun 2020 09:26:52: 3000000 INFO @ Tue, 16 Jun 2020 09:26:58: 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 09:27:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085339/SRX4085339.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085339/SRX4085339.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085339/SRX4085339.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085339/SRX4085339.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 09:27:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:27:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:27:04: 5000000 INFO @ Tue, 16 Jun 2020 09:27:09: 1000000 INFO @ Tue, 16 Jun 2020 09:27:11: 6000000 INFO @ Tue, 16 Jun 2020 09:27:15: 2000000 INFO @ Tue, 16 Jun 2020 09:27:17: 7000000 INFO @ Tue, 16 Jun 2020 09:27:20: 3000000 INFO @ Tue, 16 Jun 2020 09:27:24: 8000000 INFO @ Tue, 16 Jun 2020 09:27:26: 4000000 INFO @ Tue, 16 Jun 2020 09:27:30: 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 09:27:32: 5000000 INFO @ Tue, 16 Jun 2020 09:27:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085339/SRX4085339.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085339/SRX4085339.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085339/SRX4085339.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085339/SRX4085339.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 09:27:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:27:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:27:37: 10000000 INFO @ Tue, 16 Jun 2020 09:27:38: 6000000 INFO @ Tue, 16 Jun 2020 09:27:39: 1000000 INFO @ Tue, 16 Jun 2020 09:27:43: 11000000 INFO @ Tue, 16 Jun 2020 09:27:43: 7000000 INFO @ Tue, 16 Jun 2020 09:27:45: 2000000 INFO @ Tue, 16 Jun 2020 09:27:49: 8000000 INFO @ Tue, 16 Jun 2020 09:27:49: 12000000 INFO @ Tue, 16 Jun 2020 09:27:50: 3000000 INFO @ Tue, 16 Jun 2020 09:27:55: 9000000 INFO @ Tue, 16 Jun 2020 09:27:55: 13000000 INFO @ Tue, 16 Jun 2020 09:27:56: 4000000 INFO @ Tue, 16 Jun 2020 09:28:00: 10000000 INFO @ Tue, 16 Jun 2020 09:28:02: 14000000 INFO @ Tue, 16 Jun 2020 09:28:02: 5000000 INFO @ Tue, 16 Jun 2020 09:28:06: 11000000 INFO @ Tue, 16 Jun 2020 09:28:07: 6000000 INFO @ Tue, 16 Jun 2020 09:28:08: 15000000 INFO @ Tue, 16 Jun 2020 09:28:12: 12000000 INFO @ Tue, 16 Jun 2020 09:28:13: 7000000 INFO @ Tue, 16 Jun 2020 09:28:15: 16000000 INFO @ Tue, 16 Jun 2020 09:28:17: 13000000 INFO @ Tue, 16 Jun 2020 09:28:19: 8000000 INFO @ Tue, 16 Jun 2020 09:28:21: 17000000 INFO @ Tue, 16 Jun 2020 09:28:23: 14000000 INFO @ Tue, 16 Jun 2020 09:28:25: 9000000 INFO @ Tue, 16 Jun 2020 09:28:27: 18000000 INFO @ Tue, 16 Jun 2020 09:28:29: 15000000 INFO @ Tue, 16 Jun 2020 09:28:30: 10000000 INFO @ Tue, 16 Jun 2020 09:28:34: 19000000 INFO @ Tue, 16 Jun 2020 09:28:34: 16000000 INFO @ Tue, 16 Jun 2020 09:28:36: 11000000 INFO @ Tue, 16 Jun 2020 09:28:40: 20000000 INFO @ Tue, 16 Jun 2020 09:28:40: 17000000 INFO @ Tue, 16 Jun 2020 09:28:41: 12000000 INFO @ Tue, 16 Jun 2020 09:28:46: 18000000 INFO @ Tue, 16 Jun 2020 09:28:46: 21000000 INFO @ Tue, 16 Jun 2020 09:28:47: 13000000 INFO @ Tue, 16 Jun 2020 09:28:51: 19000000 INFO @ Tue, 16 Jun 2020 09:28:52: 14000000 INFO @ Tue, 16 Jun 2020 09:28:52: 22000000 INFO @ Tue, 16 Jun 2020 09:28:56: 20000000 INFO @ Tue, 16 Jun 2020 09:28:58: 15000000 INFO @ Tue, 16 Jun 2020 09:28:59: 23000000 INFO @ Tue, 16 Jun 2020 09:29:02: 21000000 INFO @ Tue, 16 Jun 2020 09:29:03: 16000000 INFO @ Tue, 16 Jun 2020 09:29:05: 24000000 INFO @ Tue, 16 Jun 2020 09:29:07: 22000000 INFO @ Tue, 16 Jun 2020 09:29:09: 17000000 INFO @ Tue, 16 Jun 2020 09:29:11: 25000000 INFO @ Tue, 16 Jun 2020 09:29:13: 23000000 INFO @ Tue, 16 Jun 2020 09:29:14: 18000000 INFO @ Tue, 16 Jun 2020 09:29:17: 26000000 INFO @ Tue, 16 Jun 2020 09:29:19: 24000000 INFO @ Tue, 16 Jun 2020 09:29:20: 19000000 INFO @ Tue, 16 Jun 2020 09:29:23: 27000000 INFO @ Tue, 16 Jun 2020 09:29:24: 25000000 INFO @ Tue, 16 Jun 2020 09:29:25: 20000000 INFO @ Tue, 16 Jun 2020 09:29:29: 28000000 INFO @ Tue, 16 Jun 2020 09:29:30: 26000000 INFO @ Tue, 16 Jun 2020 09:29:31: 21000000 INFO @ Tue, 16 Jun 2020 09:29:34: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:29:34: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:29:34: #1 total tags in treatment: 13780106 INFO @ Tue, 16 Jun 2020 09:29:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:29:34: #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 09:29:35: #1 tags after filtering in treatment: 11952512 INFO @ Tue, 16 Jun 2020 09:29:35: #1 Redundant rate of treatment: 0.13 INFO @ Tue, 16 Jun 2020 09:29:35: #1 finished! INFO @ Tue, 16 Jun 2020 09:29:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:29:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:29:35: 27000000 INFO @ Tue, 16 Jun 2020 09:29:35: #2 number of paired peaks: 317 WARNING @ Tue, 16 Jun 2020 09:29:35: Fewer paired peaks (317) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 317 pairs to build model! INFO @ Tue, 16 Jun 2020 09:29:35: start model_add_line... INFO @ Tue, 16 Jun 2020 09:29:35: start X-correlation... INFO @ Tue, 16 Jun 2020 09:29:35: end of X-cor INFO @ Tue, 16 Jun 2020 09:29:35: #2 finished! INFO @ Tue, 16 Jun 2020 09:29:35: #2 predicted fragment length is 142 bps INFO @ Tue, 16 Jun 2020 09:29:35: #2 alternative fragment length(s) may be 4,123,142 bps INFO @ Tue, 16 Jun 2020 09:29:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085339/SRX4085339.05_model.r INFO @ Tue, 16 Jun 2020 09:29:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:29:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:29:37: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:29:40: 28000000 INFO @ Tue, 16 Jun 2020 09:29:42: 23000000 INFO @ Tue, 16 Jun 2020 09:29:45: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:29:45: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:29:45: #1 total tags in treatment: 13780106 INFO @ Tue, 16 Jun 2020 09:29:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:29:45: #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 09:29:46: #1 tags after filtering in treatment: 11952512 INFO @ Tue, 16 Jun 2020 09:29:46: #1 Redundant rate of treatment: 0.13 INFO @ Tue, 16 Jun 2020 09:29:46: #1 finished! INFO @ Tue, 16 Jun 2020 09:29:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:29:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:29:47: #2 number of paired peaks: 317 WARNING @ Tue, 16 Jun 2020 09:29:47: Fewer paired peaks (317) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 317 pairs to build model! INFO @ Tue, 16 Jun 2020 09:29:47: start model_add_line... INFO @ Tue, 16 Jun 2020 09:29:47: start X-correlation... INFO @ Tue, 16 Jun 2020 09:29:47: end of X-cor INFO @ Tue, 16 Jun 2020 09:29:47: #2 finished! INFO @ Tue, 16 Jun 2020 09:29:47: #2 predicted fragment length is 142 bps INFO @ Tue, 16 Jun 2020 09:29:47: #2 alternative fragment length(s) may be 4,123,142 bps INFO @ Tue, 16 Jun 2020 09:29:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085339/SRX4085339.10_model.r INFO @ Tue, 16 Jun 2020 09:29:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:29:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:29:47: 24000000 INFO @ Tue, 16 Jun 2020 09:29:52: 25000000 INFO @ Tue, 16 Jun 2020 09:29:57: 26000000 INFO @ Tue, 16 Jun 2020 09:29:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:30:02: 27000000 INFO @ Tue, 16 Jun 2020 09:30:07: 28000000 INFO @ Tue, 16 Jun 2020 09:30:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085339/SRX4085339.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:30:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085339/SRX4085339.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:30:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085339/SRX4085339.05_summits.bed INFO @ Tue, 16 Jun 2020 09:30:09: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (625 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:30:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:30:12: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:30:12: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:30:12: #1 total tags in treatment: 13780106 INFO @ Tue, 16 Jun 2020 09:30:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:30:12: #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 09:30:12: #1 tags after filtering in treatment: 11952512 INFO @ Tue, 16 Jun 2020 09:30:12: #1 Redundant rate of treatment: 0.13 INFO @ Tue, 16 Jun 2020 09:30:12: #1 finished! INFO @ Tue, 16 Jun 2020 09:30:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:30:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:30:13: #2 number of paired peaks: 317 WARNING @ Tue, 16 Jun 2020 09:30:13: Fewer paired peaks (317) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 317 pairs to build model! INFO @ Tue, 16 Jun 2020 09:30:13: start model_add_line... INFO @ Tue, 16 Jun 2020 09:30:13: start X-correlation... INFO @ Tue, 16 Jun 2020 09:30:13: end of X-cor INFO @ Tue, 16 Jun 2020 09:30:13: #2 finished! INFO @ Tue, 16 Jun 2020 09:30:13: #2 predicted fragment length is 142 bps INFO @ Tue, 16 Jun 2020 09:30:13: #2 alternative fragment length(s) may be 4,123,142 bps INFO @ Tue, 16 Jun 2020 09:30:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085339/SRX4085339.20_model.r INFO @ Tue, 16 Jun 2020 09:30:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:30:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:30:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085339/SRX4085339.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:30:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085339/SRX4085339.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:30:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085339/SRX4085339.10_summits.bed INFO @ Tue, 16 Jun 2020 09:30:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (388 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:30:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:30:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085339/SRX4085339.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:30:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085339/SRX4085339.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:30:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085339/SRX4085339.20_summits.bed INFO @ Tue, 16 Jun 2020 09:30:47: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (217 records, 4 fields): 1 millis CompletedMACS2peakCalling