Job ID = 6367835 SRX = SRX4085403 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:34:20 prefetch.2.10.7: 1) Downloading 'SRR7167432'... 2020-06-15T23:34:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:00:27 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:00:27 prefetch.2.10.7: 1) 'SRR7167432' was downloaded successfully Read 85721229 spots for SRR7167432/SRR7167432.sra Written 85721229 spots for SRR7167432/SRR7167432.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: 00:59:22 85721229 reads; of these: 85721229 (100.00%) were paired; of these: 5546239 (6.47%) aligned concordantly 0 times 72812795 (84.94%) aligned concordantly exactly 1 time 7362195 (8.59%) aligned concordantly >1 times ---- 5546239 pairs aligned concordantly 0 times; of these: 410790 (7.41%) aligned discordantly 1 time ---- 5135449 pairs aligned 0 times concordantly or discordantly; of these: 10270898 mates make up the pairs; of these: 7596294 (73.96%) aligned 0 times 2217934 (21.59%) aligned exactly 1 time 456670 (4.45%) aligned >1 times 95.57% overall alignment rate Time searching: 00:59:22 Overall time: 00:59:22 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 68 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] 66383713 / 80476673 = 0.8249 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 10:36:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085403/SRX4085403.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085403/SRX4085403.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085403/SRX4085403.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085403/SRX4085403.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 10:36:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:36:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:36:34: 1000000 INFO @ Tue, 16 Jun 2020 10:36:41: 2000000 INFO @ Tue, 16 Jun 2020 10:36:48: 3000000 INFO @ Tue, 16 Jun 2020 10:36:54: 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 10:36:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085403/SRX4085403.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085403/SRX4085403.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085403/SRX4085403.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085403/SRX4085403.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 10:36:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:36:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:37:01: 5000000 INFO @ Tue, 16 Jun 2020 10:37:04: 1000000 INFO @ Tue, 16 Jun 2020 10:37:08: 6000000 INFO @ Tue, 16 Jun 2020 10:37:12: 2000000 INFO @ Tue, 16 Jun 2020 10:37:15: 7000000 INFO @ Tue, 16 Jun 2020 10:37:19: 3000000 INFO @ Tue, 16 Jun 2020 10:37:22: 8000000 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 10:37:26: 4000000 INFO @ Tue, 16 Jun 2020 10:37:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085403/SRX4085403.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085403/SRX4085403.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085403/SRX4085403.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085403/SRX4085403.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 10:37:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:37:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:37:30: 9000000 INFO @ Tue, 16 Jun 2020 10:37:33: 5000000 INFO @ Tue, 16 Jun 2020 10:37:34: 1000000 INFO @ Tue, 16 Jun 2020 10:37:37: 10000000 INFO @ Tue, 16 Jun 2020 10:37:41: 6000000 INFO @ Tue, 16 Jun 2020 10:37:41: 2000000 INFO @ Tue, 16 Jun 2020 10:37:45: 11000000 INFO @ Tue, 16 Jun 2020 10:37:48: 3000000 INFO @ Tue, 16 Jun 2020 10:37:49: 7000000 INFO @ Tue, 16 Jun 2020 10:37:53: 12000000 INFO @ Tue, 16 Jun 2020 10:37:55: 4000000 INFO @ Tue, 16 Jun 2020 10:37:56: 8000000 INFO @ Tue, 16 Jun 2020 10:38:00: 13000000 INFO @ Tue, 16 Jun 2020 10:38:02: 5000000 INFO @ Tue, 16 Jun 2020 10:38:04: 9000000 INFO @ Tue, 16 Jun 2020 10:38:08: 14000000 INFO @ Tue, 16 Jun 2020 10:38:09: 6000000 INFO @ Tue, 16 Jun 2020 10:38:11: 10000000 INFO @ Tue, 16 Jun 2020 10:38:15: 15000000 INFO @ Tue, 16 Jun 2020 10:38:16: 7000000 INFO @ Tue, 16 Jun 2020 10:38:19: 11000000 INFO @ Tue, 16 Jun 2020 10:38:22: 8000000 INFO @ Tue, 16 Jun 2020 10:38:23: 16000000 INFO @ Tue, 16 Jun 2020 10:38:26: 12000000 INFO @ Tue, 16 Jun 2020 10:38:29: 9000000 INFO @ Tue, 16 Jun 2020 10:38:30: 17000000 INFO @ Tue, 16 Jun 2020 10:38:34: 13000000 INFO @ Tue, 16 Jun 2020 10:38:36: 10000000 INFO @ Tue, 16 Jun 2020 10:38:38: 18000000 INFO @ Tue, 16 Jun 2020 10:38:42: 14000000 INFO @ Tue, 16 Jun 2020 10:38:43: 11000000 INFO @ Tue, 16 Jun 2020 10:38:45: 19000000 INFO @ Tue, 16 Jun 2020 10:38:49: 15000000 INFO @ Tue, 16 Jun 2020 10:38:49: 12000000 INFO @ Tue, 16 Jun 2020 10:38:53: 20000000 INFO @ Tue, 16 Jun 2020 10:38:56: 13000000 INFO @ Tue, 16 Jun 2020 10:38:57: 16000000 INFO @ Tue, 16 Jun 2020 10:39:01: 21000000 INFO @ Tue, 16 Jun 2020 10:39:03: 14000000 INFO @ Tue, 16 Jun 2020 10:39:04: 17000000 INFO @ Tue, 16 Jun 2020 10:39:08: 22000000 INFO @ Tue, 16 Jun 2020 10:39:10: 15000000 INFO @ Tue, 16 Jun 2020 10:39:12: 18000000 INFO @ Tue, 16 Jun 2020 10:39:16: 23000000 INFO @ Tue, 16 Jun 2020 10:39:17: 16000000 INFO @ Tue, 16 Jun 2020 10:39:19: 19000000 INFO @ Tue, 16 Jun 2020 10:39:23: 24000000 INFO @ Tue, 16 Jun 2020 10:39:24: 17000000 INFO @ Tue, 16 Jun 2020 10:39:27: 20000000 INFO @ Tue, 16 Jun 2020 10:39:31: 25000000 INFO @ Tue, 16 Jun 2020 10:39:31: 18000000 INFO @ Tue, 16 Jun 2020 10:39:35: 21000000 INFO @ Tue, 16 Jun 2020 10:39:39: 26000000 INFO @ Tue, 16 Jun 2020 10:39:39: 19000000 INFO @ Tue, 16 Jun 2020 10:39:42: 22000000 INFO @ Tue, 16 Jun 2020 10:39:46: 20000000 INFO @ Tue, 16 Jun 2020 10:39:46: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:39:50: 23000000 INFO @ Tue, 16 Jun 2020 10:39:54: 28000000 INFO @ Tue, 16 Jun 2020 10:39:54: 21000000 INFO @ Tue, 16 Jun 2020 10:39:58: 24000000 INFO @ Tue, 16 Jun 2020 10:40:01: 29000000 INFO @ Tue, 16 Jun 2020 10:40:01: 22000000 INFO @ Tue, 16 Jun 2020 10:40:05: 25000000 INFO @ Tue, 16 Jun 2020 10:40:08: 30000000 INFO @ Tue, 16 Jun 2020 10:40:09: 23000000 INFO @ Tue, 16 Jun 2020 10:40:13: 26000000 INFO @ Tue, 16 Jun 2020 10:40:15: 31000000 INFO @ Tue, 16 Jun 2020 10:40:16: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 10:40:16: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 10:40:16: #1 total tags in treatment: 14030341 INFO @ Tue, 16 Jun 2020 10:40:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:40:16: #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 10:40:16: #1 tags after filtering in treatment: 10518920 INFO @ Tue, 16 Jun 2020 10:40:16: #1 Redundant rate of treatment: 0.25 INFO @ Tue, 16 Jun 2020 10:40:16: #1 finished! INFO @ Tue, 16 Jun 2020 10:40:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:40:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:40:17: 24000000 INFO @ Tue, 16 Jun 2020 10:40:17: #2 number of paired peaks: 761 WARNING @ Tue, 16 Jun 2020 10:40:17: Fewer paired peaks (761) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 761 pairs to build model! INFO @ Tue, 16 Jun 2020 10:40:17: start model_add_line... INFO @ Tue, 16 Jun 2020 10:40:17: start X-correlation... INFO @ Tue, 16 Jun 2020 10:40:17: end of X-cor INFO @ Tue, 16 Jun 2020 10:40:17: #2 finished! INFO @ Tue, 16 Jun 2020 10:40:17: #2 predicted fragment length is 103 bps INFO @ Tue, 16 Jun 2020 10:40:17: #2 alternative fragment length(s) may be 103 bps INFO @ Tue, 16 Jun 2020 10:40:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085403/SRX4085403.05_model.r INFO @ Tue, 16 Jun 2020 10:40:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:40:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:40:21: 27000000 INFO @ Tue, 16 Jun 2020 10:40:24: 25000000 INFO @ Tue, 16 Jun 2020 10:40:27: 28000000 INFO @ Tue, 16 Jun 2020 10:40:31: 26000000 INFO @ Tue, 16 Jun 2020 10:40:33: 29000000 INFO @ Tue, 16 Jun 2020 10:40:37: 27000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:40:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:40:39: 30000000 INFO @ Tue, 16 Jun 2020 10:40:43: 28000000 INFO @ Tue, 16 Jun 2020 10:40:45: 31000000 INFO @ Tue, 16 Jun 2020 10:40:46: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 10:40:46: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 10:40:46: #1 total tags in treatment: 14030341 INFO @ Tue, 16 Jun 2020 10:40:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:40:46: #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 10:40:46: #1 tags after filtering in treatment: 10518920 INFO @ Tue, 16 Jun 2020 10:40:46: #1 Redundant rate of treatment: 0.25 INFO @ Tue, 16 Jun 2020 10:40:46: #1 finished! INFO @ Tue, 16 Jun 2020 10:40:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:40:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:40:47: #2 number of paired peaks: 761 WARNING @ Tue, 16 Jun 2020 10:40:47: Fewer paired peaks (761) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 761 pairs to build model! INFO @ Tue, 16 Jun 2020 10:40:47: start model_add_line... INFO @ Tue, 16 Jun 2020 10:40:47: start X-correlation... INFO @ Tue, 16 Jun 2020 10:40:47: end of X-cor INFO @ Tue, 16 Jun 2020 10:40:47: #2 finished! INFO @ Tue, 16 Jun 2020 10:40:47: #2 predicted fragment length is 103 bps INFO @ Tue, 16 Jun 2020 10:40:47: #2 alternative fragment length(s) may be 103 bps INFO @ Tue, 16 Jun 2020 10:40:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085403/SRX4085403.10_model.r INFO @ Tue, 16 Jun 2020 10:40:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:40:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:40:49: 29000000 INFO @ Tue, 16 Jun 2020 10:40:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085403/SRX4085403.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:40:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085403/SRX4085403.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:40:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085403/SRX4085403.05_summits.bed INFO @ Tue, 16 Jun 2020 10:40:51: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4915 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:40:54: 30000000 INFO @ Tue, 16 Jun 2020 10:41:00: 31000000 INFO @ Tue, 16 Jun 2020 10:41:00: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 10:41:00: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 10:41:00: #1 total tags in treatment: 14030341 INFO @ Tue, 16 Jun 2020 10:41:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:41:00: #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 10:41:00: #1 tags after filtering in treatment: 10518920 INFO @ Tue, 16 Jun 2020 10:41:00: #1 Redundant rate of treatment: 0.25 INFO @ Tue, 16 Jun 2020 10:41:00: #1 finished! INFO @ Tue, 16 Jun 2020 10:41:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:41:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:41:01: #2 number of paired peaks: 761 WARNING @ Tue, 16 Jun 2020 10:41:01: Fewer paired peaks (761) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 761 pairs to build model! INFO @ Tue, 16 Jun 2020 10:41:01: start model_add_line... INFO @ Tue, 16 Jun 2020 10:41:01: start X-correlation... INFO @ Tue, 16 Jun 2020 10:41:01: end of X-cor INFO @ Tue, 16 Jun 2020 10:41:01: #2 finished! INFO @ Tue, 16 Jun 2020 10:41:01: #2 predicted fragment length is 103 bps INFO @ Tue, 16 Jun 2020 10:41:01: #2 alternative fragment length(s) may be 103 bps INFO @ Tue, 16 Jun 2020 10:41:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085403/SRX4085403.20_model.r INFO @ Tue, 16 Jun 2020 10:41:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:41:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:41:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:41:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085403/SRX4085403.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:41:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085403/SRX4085403.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:41:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085403/SRX4085403.10_summits.bed INFO @ Tue, 16 Jun 2020 10:41:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3091 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:41:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:41:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085403/SRX4085403.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:41:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085403/SRX4085403.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:41:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085403/SRX4085403.20_summits.bed INFO @ Tue, 16 Jun 2020 10:41:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1753 records, 4 fields): 3 millis CompletedMACS2peakCalling