Job ID = 6367831 SRX = SRX4085399 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:46:48 prefetch.2.10.7: 1) Downloading 'SRR7167428'... 2020-06-15T23:46:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:55:09 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:55:09 prefetch.2.10.7: 1) 'SRR7167428' was downloaded successfully Read 32931163 spots for SRR7167428/SRR7167428.sra Written 32931163 spots for SRR7167428/SRR7167428.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: 00:26:20 32931163 reads; of these: 32931163 (100.00%) were paired; of these: 1116191 (3.39%) aligned concordantly 0 times 28116566 (85.38%) aligned concordantly exactly 1 time 3698406 (11.23%) aligned concordantly >1 times ---- 1116191 pairs aligned concordantly 0 times; of these: 321334 (28.79%) aligned discordantly 1 time ---- 794857 pairs aligned 0 times concordantly or discordantly; of these: 1589714 mates make up the pairs; of these: 880093 (55.36%) aligned 0 times 519596 (32.68%) aligned exactly 1 time 190025 (11.95%) aligned >1 times 98.66% overall alignment rate Time searching: 00:26:20 Overall time: 00:26:20 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 28 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] 20145648 / 31917223 = 0.6312 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 09:37:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085399/SRX4085399.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085399/SRX4085399.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085399/SRX4085399.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085399/SRX4085399.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 09:37:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:37:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:37:46: 1000000 INFO @ Tue, 16 Jun 2020 09:37:51: 2000000 INFO @ Tue, 16 Jun 2020 09:37:56: 3000000 INFO @ Tue, 16 Jun 2020 09:38:01: 4000000 INFO @ Tue, 16 Jun 2020 09:38:06: 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 @ Tue, 16 Jun 2020 09:38:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085399/SRX4085399.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085399/SRX4085399.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085399/SRX4085399.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085399/SRX4085399.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 09:38:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:38:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:38:11: 6000000 INFO @ Tue, 16 Jun 2020 09:38:16: 1000000 INFO @ Tue, 16 Jun 2020 09:38:16: 7000000 INFO @ Tue, 16 Jun 2020 09:38:21: 8000000 INFO @ Tue, 16 Jun 2020 09:38:21: 2000000 INFO @ Tue, 16 Jun 2020 09:38:27: 9000000 INFO @ Tue, 16 Jun 2020 09:38:27: 3000000 INFO @ Tue, 16 Jun 2020 09:38:32: 10000000 INFO @ Tue, 16 Jun 2020 09:38:32: 4000000 INFO @ Tue, 16 Jun 2020 09:38:37: 11000000 INFO @ Tue, 16 Jun 2020 09:38:38: 5000000 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 09:38:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085399/SRX4085399.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085399/SRX4085399.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085399/SRX4085399.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085399/SRX4085399.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 09:38:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:38:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:38:42: 12000000 INFO @ Tue, 16 Jun 2020 09:38:43: 6000000 INFO @ Tue, 16 Jun 2020 09:38:46: 1000000 INFO @ Tue, 16 Jun 2020 09:38:48: 13000000 INFO @ Tue, 16 Jun 2020 09:38:48: 7000000 INFO @ Tue, 16 Jun 2020 09:38:52: 2000000 INFO @ Tue, 16 Jun 2020 09:38:53: 14000000 INFO @ Tue, 16 Jun 2020 09:38:54: 8000000 INFO @ Tue, 16 Jun 2020 09:38:57: 3000000 INFO @ Tue, 16 Jun 2020 09:38:58: 15000000 INFO @ Tue, 16 Jun 2020 09:38:59: 9000000 INFO @ Tue, 16 Jun 2020 09:39:03: 4000000 INFO @ Tue, 16 Jun 2020 09:39:04: 16000000 INFO @ Tue, 16 Jun 2020 09:39:04: 10000000 INFO @ Tue, 16 Jun 2020 09:39:08: 5000000 INFO @ Tue, 16 Jun 2020 09:39:09: 17000000 INFO @ Tue, 16 Jun 2020 09:39:10: 11000000 INFO @ Tue, 16 Jun 2020 09:39:13: 6000000 INFO @ Tue, 16 Jun 2020 09:39:14: 18000000 INFO @ Tue, 16 Jun 2020 09:39:15: 12000000 INFO @ Tue, 16 Jun 2020 09:39:19: 7000000 INFO @ Tue, 16 Jun 2020 09:39:19: 19000000 INFO @ Tue, 16 Jun 2020 09:39:20: 13000000 INFO @ Tue, 16 Jun 2020 09:39:24: 8000000 INFO @ Tue, 16 Jun 2020 09:39:25: 20000000 INFO @ Tue, 16 Jun 2020 09:39:26: 14000000 INFO @ Tue, 16 Jun 2020 09:39:30: 21000000 INFO @ Tue, 16 Jun 2020 09:39:30: 9000000 INFO @ Tue, 16 Jun 2020 09:39:31: 15000000 INFO @ Tue, 16 Jun 2020 09:39:35: 22000000 INFO @ Tue, 16 Jun 2020 09:39:35: 10000000 INFO @ Tue, 16 Jun 2020 09:39:36: 16000000 INFO @ Tue, 16 Jun 2020 09:39:40: 23000000 INFO @ Tue, 16 Jun 2020 09:39:40: 11000000 INFO @ Tue, 16 Jun 2020 09:39:41: 17000000 INFO @ Tue, 16 Jun 2020 09:39:45: 24000000 INFO @ Tue, 16 Jun 2020 09:39:46: 12000000 INFO @ Tue, 16 Jun 2020 09:39:47: 18000000 INFO @ Tue, 16 Jun 2020 09:39:49: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:39:49: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:39:49: #1 total tags in treatment: 11723541 INFO @ Tue, 16 Jun 2020 09:39:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:39:49: #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 09:39:49: #1 tags after filtering in treatment: 10231883 INFO @ Tue, 16 Jun 2020 09:39:49: #1 Redundant rate of treatment: 0.13 INFO @ Tue, 16 Jun 2020 09:39:49: #1 finished! INFO @ Tue, 16 Jun 2020 09:39:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:39:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:39:50: #2 number of paired peaks: 324 WARNING @ Tue, 16 Jun 2020 09:39:50: Fewer paired peaks (324) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 324 pairs to build model! INFO @ Tue, 16 Jun 2020 09:39:50: start model_add_line... INFO @ Tue, 16 Jun 2020 09:39:50: start X-correlation... INFO @ Tue, 16 Jun 2020 09:39:50: end of X-cor INFO @ Tue, 16 Jun 2020 09:39:50: #2 finished! INFO @ Tue, 16 Jun 2020 09:39:50: #2 predicted fragment length is 117 bps INFO @ Tue, 16 Jun 2020 09:39:50: #2 alternative fragment length(s) may be 3,117 bps INFO @ Tue, 16 Jun 2020 09:39:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085399/SRX4085399.05_model.r INFO @ Tue, 16 Jun 2020 09:39:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:39:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:39:51: 13000000 INFO @ Tue, 16 Jun 2020 09:39:52: 19000000 INFO @ Tue, 16 Jun 2020 09:39:56: 14000000 INFO @ Tue, 16 Jun 2020 09:39:57: 20000000 INFO @ Tue, 16 Jun 2020 09:40:01: 15000000 INFO @ Tue, 16 Jun 2020 09:40:03: 21000000 INFO @ Tue, 16 Jun 2020 09:40:07: 16000000 INFO @ Tue, 16 Jun 2020 09:40:08: 22000000 INFO @ Tue, 16 Jun 2020 09:40:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:40:12: 17000000 INFO @ Tue, 16 Jun 2020 09:40:13: 23000000 INFO @ Tue, 16 Jun 2020 09:40:17: 18000000 INFO @ Tue, 16 Jun 2020 09:40:18: 24000000 INFO @ Tue, 16 Jun 2020 09:40:22: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:40:22: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:40:22: #1 total tags in treatment: 11723541 INFO @ Tue, 16 Jun 2020 09:40:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:40:22: #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 09:40:22: #1 tags after filtering in treatment: 10231883 INFO @ Tue, 16 Jun 2020 09:40:22: #1 Redundant rate of treatment: 0.13 INFO @ Tue, 16 Jun 2020 09:40:22: #1 finished! INFO @ Tue, 16 Jun 2020 09:40:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:40:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:40:22: 19000000 INFO @ Tue, 16 Jun 2020 09:40:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085399/SRX4085399.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:40:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085399/SRX4085399.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:40:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085399/SRX4085399.05_summits.bed INFO @ Tue, 16 Jun 2020 09:40:22: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (2424 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:40:23: #2 number of paired peaks: 324 WARNING @ Tue, 16 Jun 2020 09:40:23: Fewer paired peaks (324) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 324 pairs to build model! INFO @ Tue, 16 Jun 2020 09:40:23: start model_add_line... INFO @ Tue, 16 Jun 2020 09:40:23: start X-correlation... INFO @ Tue, 16 Jun 2020 09:40:23: end of X-cor INFO @ Tue, 16 Jun 2020 09:40:23: #2 finished! INFO @ Tue, 16 Jun 2020 09:40:23: #2 predicted fragment length is 117 bps INFO @ Tue, 16 Jun 2020 09:40:23: #2 alternative fragment length(s) may be 3,117 bps INFO @ Tue, 16 Jun 2020 09:40:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085399/SRX4085399.10_model.r INFO @ Tue, 16 Jun 2020 09:40:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:40:23: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:40:27: 20000000 INFO @ Tue, 16 Jun 2020 09:40:32: 21000000 INFO @ Tue, 16 Jun 2020 09:40:37: 22000000 INFO @ Tue, 16 Jun 2020 09:40:42: 23000000 INFO @ Tue, 16 Jun 2020 09:40:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:40:47: 24000000 INFO @ Tue, 16 Jun 2020 09:40:50: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:40:50: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:40:50: #1 total tags in treatment: 11723541 INFO @ Tue, 16 Jun 2020 09:40:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:40:50: #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 09:40:50: #1 tags after filtering in treatment: 10231883 INFO @ Tue, 16 Jun 2020 09:40:50: #1 Redundant rate of treatment: 0.13 INFO @ Tue, 16 Jun 2020 09:40:50: #1 finished! INFO @ Tue, 16 Jun 2020 09:40:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:40:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:40:51: #2 number of paired peaks: 324 WARNING @ Tue, 16 Jun 2020 09:40:51: Fewer paired peaks (324) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 324 pairs to build model! INFO @ Tue, 16 Jun 2020 09:40:51: start model_add_line... INFO @ Tue, 16 Jun 2020 09:40:51: start X-correlation... INFO @ Tue, 16 Jun 2020 09:40:51: end of X-cor INFO @ Tue, 16 Jun 2020 09:40:51: #2 finished! INFO @ Tue, 16 Jun 2020 09:40:51: #2 predicted fragment length is 117 bps INFO @ Tue, 16 Jun 2020 09:40:51: #2 alternative fragment length(s) may be 3,117 bps INFO @ Tue, 16 Jun 2020 09:40:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085399/SRX4085399.20_model.r INFO @ Tue, 16 Jun 2020 09:40:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:40:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:40:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085399/SRX4085399.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:40:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085399/SRX4085399.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:40:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085399/SRX4085399.10_summits.bed INFO @ Tue, 16 Jun 2020 09:40:56: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (748 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:41:12: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:41:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085399/SRX4085399.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:41:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085399/SRX4085399.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:41:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085399/SRX4085399.20_summits.bed INFO @ Tue, 16 Jun 2020 09:41:23: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (197 records, 4 fields): 1 millis CompletedMACS2peakCalling