Job ID = 6507730 SRX = SRX1353667 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T13:44:31 prefetch.2.10.7: 1) Downloading 'SRR2722821'... 2020-06-26T13:44:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:47:20 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:47:20 prefetch.2.10.7: 1) 'SRR2722821' was downloaded successfully Read 15113259 spots for SRR2722821/SRR2722821.sra Written 15113259 spots for SRR2722821/SRR2722821.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: 00:13:00 15113259 reads; of these: 15113259 (100.00%) were paired; of these: 909625 (6.02%) aligned concordantly 0 times 12097298 (80.04%) aligned concordantly exactly 1 time 2106336 (13.94%) aligned concordantly >1 times ---- 909625 pairs aligned concordantly 0 times; of these: 288672 (31.74%) aligned discordantly 1 time ---- 620953 pairs aligned 0 times concordantly or discordantly; of these: 1241906 mates make up the pairs; of these: 847922 (68.28%) aligned 0 times 251813 (20.28%) aligned exactly 1 time 142171 (11.45%) aligned >1 times 97.19% overall alignment rate Time searching: 00:13:00 Overall time: 00:13:00 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] 278185 / 14400392 = 0.0193 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 23:10:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1353667/SRX1353667.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1353667/SRX1353667.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1353667/SRX1353667.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1353667/SRX1353667.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 23:10:12: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:10:12: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:10:17: 1000000 INFO @ Fri, 26 Jun 2020 23:10:21: 2000000 INFO @ Fri, 26 Jun 2020 23:10:25: 3000000 INFO @ Fri, 26 Jun 2020 23:10:30: 4000000 INFO @ Fri, 26 Jun 2020 23:10:34: 5000000 INFO @ Fri, 26 Jun 2020 23:10:38: 6000000 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 23:10:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1353667/SRX1353667.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1353667/SRX1353667.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1353667/SRX1353667.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1353667/SRX1353667.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 23:10:42: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:10:42: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:10:42: 7000000 INFO @ Fri, 26 Jun 2020 23:10:47: 8000000 INFO @ Fri, 26 Jun 2020 23:10:47: 1000000 INFO @ Fri, 26 Jun 2020 23:10:51: 9000000 INFO @ Fri, 26 Jun 2020 23:10:51: 2000000 INFO @ Fri, 26 Jun 2020 23:10:56: 3000000 INFO @ Fri, 26 Jun 2020 23:10:56: 10000000 INFO @ Fri, 26 Jun 2020 23:11:00: 4000000 INFO @ Fri, 26 Jun 2020 23:11:00: 11000000 INFO @ Fri, 26 Jun 2020 23:11:04: 5000000 INFO @ Fri, 26 Jun 2020 23:11:05: 12000000 INFO @ Fri, 26 Jun 2020 23:11:09: 6000000 INFO @ Fri, 26 Jun 2020 23:11:09: 13000000 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 23:11:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1353667/SRX1353667.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1353667/SRX1353667.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1353667/SRX1353667.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1353667/SRX1353667.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 23:11:12: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:11:12: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:11:13: 7000000 INFO @ Fri, 26 Jun 2020 23:11:14: 14000000 INFO @ Fri, 26 Jun 2020 23:11:17: 1000000 INFO @ Fri, 26 Jun 2020 23:11:17: 8000000 INFO @ Fri, 26 Jun 2020 23:11:18: 15000000 INFO @ Fri, 26 Jun 2020 23:11:21: 2000000 INFO @ Fri, 26 Jun 2020 23:11:22: 9000000 INFO @ Fri, 26 Jun 2020 23:11:23: 16000000 INFO @ Fri, 26 Jun 2020 23:11:26: 3000000 INFO @ Fri, 26 Jun 2020 23:11:26: 10000000 INFO @ Fri, 26 Jun 2020 23:11:28: 17000000 INFO @ Fri, 26 Jun 2020 23:11:30: 4000000 INFO @ Fri, 26 Jun 2020 23:11:31: 11000000 INFO @ Fri, 26 Jun 2020 23:11:32: 18000000 INFO @ Fri, 26 Jun 2020 23:11:34: 5000000 INFO @ Fri, 26 Jun 2020 23:11:35: 12000000 INFO @ Fri, 26 Jun 2020 23:11:37: 19000000 INFO @ Fri, 26 Jun 2020 23:11:39: 6000000 INFO @ Fri, 26 Jun 2020 23:11:39: 13000000 INFO @ Fri, 26 Jun 2020 23:11:41: 20000000 INFO @ Fri, 26 Jun 2020 23:11:43: 7000000 INFO @ Fri, 26 Jun 2020 23:11:44: 14000000 INFO @ Fri, 26 Jun 2020 23:11:46: 21000000 INFO @ Fri, 26 Jun 2020 23:11:48: 8000000 INFO @ Fri, 26 Jun 2020 23:11:48: 15000000 INFO @ Fri, 26 Jun 2020 23:11:50: 22000000 INFO @ Fri, 26 Jun 2020 23:11:52: 9000000 INFO @ Fri, 26 Jun 2020 23:11:53: 16000000 INFO @ Fri, 26 Jun 2020 23:11:55: 23000000 INFO @ Fri, 26 Jun 2020 23:11:56: 10000000 INFO @ Fri, 26 Jun 2020 23:11:57: 17000000 INFO @ Fri, 26 Jun 2020 23:12:00: 24000000 INFO @ Fri, 26 Jun 2020 23:12:01: 11000000 INFO @ Fri, 26 Jun 2020 23:12:02: 18000000 INFO @ Fri, 26 Jun 2020 23:12:04: 25000000 INFO @ Fri, 26 Jun 2020 23:12:05: 12000000 INFO @ Fri, 26 Jun 2020 23:12:06: 19000000 INFO @ Fri, 26 Jun 2020 23:12:09: 26000000 INFO @ Fri, 26 Jun 2020 23:12:10: 13000000 INFO @ Fri, 26 Jun 2020 23:12:10: 20000000 INFO @ Fri, 26 Jun 2020 23:12:13: 27000000 INFO @ Fri, 26 Jun 2020 23:12:14: 14000000 INFO @ Fri, 26 Jun 2020 23:12:15: 21000000 INFO @ Fri, 26 Jun 2020 23:12:18: 28000000 INFO @ Fri, 26 Jun 2020 23:12:19: 15000000 INFO @ Fri, 26 Jun 2020 23:12:19: 22000000 INFO @ Fri, 26 Jun 2020 23:12:22: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:12:22: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:12:22: #1 total tags in treatment: 13926759 INFO @ Fri, 26 Jun 2020 23:12:22: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:12:22: #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 23:12:22: #1 tags after filtering in treatment: 12919657 INFO @ Fri, 26 Jun 2020 23:12:22: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 23:12:22: #1 finished! INFO @ Fri, 26 Jun 2020 23:12:22: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:12:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:12:23: #2 number of paired peaks: 312 WARNING @ Fri, 26 Jun 2020 23:12:23: Fewer paired peaks (312) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 312 pairs to build model! INFO @ Fri, 26 Jun 2020 23:12:23: start model_add_line... INFO @ Fri, 26 Jun 2020 23:12:23: start X-correlation... INFO @ Fri, 26 Jun 2020 23:12:23: end of X-cor INFO @ Fri, 26 Jun 2020 23:12:23: #2 finished! INFO @ Fri, 26 Jun 2020 23:12:23: #2 predicted fragment length is 125 bps INFO @ Fri, 26 Jun 2020 23:12:23: #2 alternative fragment length(s) may be 4,114,125 bps INFO @ Fri, 26 Jun 2020 23:12:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1353667/SRX1353667.05_model.r INFO @ Fri, 26 Jun 2020 23:12:23: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:12:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:12:23: 16000000 INFO @ Fri, 26 Jun 2020 23:12:24: 23000000 INFO @ Fri, 26 Jun 2020 23:12:28: 17000000 INFO @ Fri, 26 Jun 2020 23:12:28: 24000000 INFO @ Fri, 26 Jun 2020 23:12:32: 18000000 INFO @ Fri, 26 Jun 2020 23:12:33: 25000000 INFO @ Fri, 26 Jun 2020 23:12:36: 19000000 INFO @ Fri, 26 Jun 2020 23:12:37: 26000000 INFO @ Fri, 26 Jun 2020 23:12:41: 20000000 INFO @ Fri, 26 Jun 2020 23:12:42: 27000000 INFO @ Fri, 26 Jun 2020 23:12:45: 21000000 INFO @ Fri, 26 Jun 2020 23:12:46: 28000000 INFO @ Fri, 26 Jun 2020 23:12:50: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:12:50: 22000000 INFO @ Fri, 26 Jun 2020 23:12:50: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:12:50: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:12:50: #1 total tags in treatment: 13926759 INFO @ Fri, 26 Jun 2020 23:12:50: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:12:50: #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 23:12:50: #1 tags after filtering in treatment: 12919657 INFO @ Fri, 26 Jun 2020 23:12:50: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 23:12:50: #1 finished! INFO @ Fri, 26 Jun 2020 23:12:50: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:12:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:12:51: #2 number of paired peaks: 312 WARNING @ Fri, 26 Jun 2020 23:12:51: Fewer paired peaks (312) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 312 pairs to build model! INFO @ Fri, 26 Jun 2020 23:12:51: start model_add_line... INFO @ Fri, 26 Jun 2020 23:12:51: start X-correlation... INFO @ Fri, 26 Jun 2020 23:12:51: end of X-cor INFO @ Fri, 26 Jun 2020 23:12:51: #2 finished! INFO @ Fri, 26 Jun 2020 23:12:51: #2 predicted fragment length is 125 bps INFO @ Fri, 26 Jun 2020 23:12:51: #2 alternative fragment length(s) may be 4,114,125 bps INFO @ Fri, 26 Jun 2020 23:12:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1353667/SRX1353667.10_model.r INFO @ Fri, 26 Jun 2020 23:12:51: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:12:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:12:54: 23000000 INFO @ Fri, 26 Jun 2020 23:12:58: 24000000 INFO @ Fri, 26 Jun 2020 23:13:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1353667/SRX1353667.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:13:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1353667/SRX1353667.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:13:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1353667/SRX1353667.05_summits.bed INFO @ Fri, 26 Jun 2020 23:13:02: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (512 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:13:03: 25000000 INFO @ Fri, 26 Jun 2020 23:13:07: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:13:11: 27000000 INFO @ Fri, 26 Jun 2020 23:13:16: 28000000 INFO @ Fri, 26 Jun 2020 23:13:17: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:13:19: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:13:19: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:13:19: #1 total tags in treatment: 13926759 INFO @ Fri, 26 Jun 2020 23:13:19: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:13:19: #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 23:13:20: #1 tags after filtering in treatment: 12919657 INFO @ Fri, 26 Jun 2020 23:13:20: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 23:13:20: #1 finished! INFO @ Fri, 26 Jun 2020 23:13:20: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:13:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:13:20: #2 number of paired peaks: 312 WARNING @ Fri, 26 Jun 2020 23:13:20: Fewer paired peaks (312) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 312 pairs to build model! INFO @ Fri, 26 Jun 2020 23:13:20: start model_add_line... INFO @ Fri, 26 Jun 2020 23:13:21: start X-correlation... INFO @ Fri, 26 Jun 2020 23:13:21: end of X-cor INFO @ Fri, 26 Jun 2020 23:13:21: #2 finished! INFO @ Fri, 26 Jun 2020 23:13:21: #2 predicted fragment length is 125 bps INFO @ Fri, 26 Jun 2020 23:13:21: #2 alternative fragment length(s) may be 4,114,125 bps INFO @ Fri, 26 Jun 2020 23:13:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1353667/SRX1353667.20_model.r INFO @ Fri, 26 Jun 2020 23:13:21: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:13:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:13:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1353667/SRX1353667.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:13:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1353667/SRX1353667.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:13:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1353667/SRX1353667.10_summits.bed INFO @ Fri, 26 Jun 2020 23:13:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (285 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:13:46: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:13:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1353667/SRX1353667.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:13:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1353667/SRX1353667.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:13:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1353667/SRX1353667.20_summits.bed INFO @ Fri, 26 Jun 2020 23:13:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (182 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。