Job ID = 6367778 SRX = SRX4085348 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:43:44 prefetch.2.10.7: 1) Downloading 'SRR7167377'... 2020-06-15T23:43:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:51:38 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:51:38 prefetch.2.10.7: 1) 'SRR7167377' was downloaded successfully Read 15383484 spots for SRR7167377/SRR7167377.sra Written 15383484 spots for SRR7167377/SRR7167377.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: 00:12:31 15383484 reads; of these: 15383484 (100.00%) were paired; of these: 1376536 (8.95%) aligned concordantly 0 times 12277327 (79.81%) aligned concordantly exactly 1 time 1729621 (11.24%) aligned concordantly >1 times ---- 1376536 pairs aligned concordantly 0 times; of these: 90460 (6.57%) aligned discordantly 1 time ---- 1286076 pairs aligned 0 times concordantly or discordantly; of these: 2572152 mates make up the pairs; of these: 1663532 (64.67%) aligned 0 times 765781 (29.77%) aligned exactly 1 time 142839 (5.55%) aligned >1 times 94.59% overall alignment rate Time searching: 00:12:31 Overall time: 00:12:31 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] 2455635 / 14076569 = 0.1744 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 09:13:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085348/SRX4085348.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085348/SRX4085348.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085348/SRX4085348.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085348/SRX4085348.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 09:13:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:13:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:13:45: 1000000 INFO @ Tue, 16 Jun 2020 09:13:51: 2000000 INFO @ Tue, 16 Jun 2020 09:13:56: 3000000 INFO @ Tue, 16 Jun 2020 09:14:02: 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 09:14:07: 5000000 INFO @ Tue, 16 Jun 2020 09:14:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085348/SRX4085348.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085348/SRX4085348.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085348/SRX4085348.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085348/SRX4085348.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 09:14:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:14:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:14:13: 6000000 INFO @ Tue, 16 Jun 2020 09:14:17: 1000000 INFO @ Tue, 16 Jun 2020 09:14:20: 7000000 INFO @ Tue, 16 Jun 2020 09:14:23: 2000000 INFO @ Tue, 16 Jun 2020 09:14:26: 8000000 INFO @ Tue, 16 Jun 2020 09:14:29: 3000000 INFO @ Tue, 16 Jun 2020 09:14:32: 9000000 INFO @ Tue, 16 Jun 2020 09:14:36: 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 09:14:39: 10000000 INFO @ Tue, 16 Jun 2020 09:14:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085348/SRX4085348.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085348/SRX4085348.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085348/SRX4085348.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085348/SRX4085348.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 09:14:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:14:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:14:42: 5000000 INFO @ Tue, 16 Jun 2020 09:14:45: 11000000 INFO @ Tue, 16 Jun 2020 09:14:46: 1000000 INFO @ Tue, 16 Jun 2020 09:14:48: 6000000 INFO @ Tue, 16 Jun 2020 09:14:51: 12000000 INFO @ Tue, 16 Jun 2020 09:14:52: 2000000 INFO @ Tue, 16 Jun 2020 09:14:55: 7000000 INFO @ Tue, 16 Jun 2020 09:14:58: 13000000 INFO @ Tue, 16 Jun 2020 09:14:59: 3000000 INFO @ Tue, 16 Jun 2020 09:15:01: 8000000 INFO @ Tue, 16 Jun 2020 09:15:05: 14000000 INFO @ Tue, 16 Jun 2020 09:15:06: 4000000 INFO @ Tue, 16 Jun 2020 09:15:08: 9000000 INFO @ Tue, 16 Jun 2020 09:15:11: 15000000 INFO @ Tue, 16 Jun 2020 09:15:13: 5000000 INFO @ Tue, 16 Jun 2020 09:15:14: 10000000 INFO @ Tue, 16 Jun 2020 09:15:18: 16000000 INFO @ Tue, 16 Jun 2020 09:15:19: 6000000 INFO @ Tue, 16 Jun 2020 09:15:21: 11000000 INFO @ Tue, 16 Jun 2020 09:15:25: 17000000 INFO @ Tue, 16 Jun 2020 09:15:26: 7000000 INFO @ Tue, 16 Jun 2020 09:15:27: 12000000 INFO @ Tue, 16 Jun 2020 09:15:31: 18000000 INFO @ Tue, 16 Jun 2020 09:15:33: 8000000 INFO @ Tue, 16 Jun 2020 09:15:34: 13000000 INFO @ Tue, 16 Jun 2020 09:15:38: 19000000 INFO @ Tue, 16 Jun 2020 09:15:40: 9000000 INFO @ Tue, 16 Jun 2020 09:15:40: 14000000 INFO @ Tue, 16 Jun 2020 09:15:44: 20000000 INFO @ Tue, 16 Jun 2020 09:15:46: 10000000 INFO @ Tue, 16 Jun 2020 09:15:47: 15000000 INFO @ Tue, 16 Jun 2020 09:15:51: 21000000 INFO @ Tue, 16 Jun 2020 09:15:53: 11000000 INFO @ Tue, 16 Jun 2020 09:15:53: 16000000 INFO @ Tue, 16 Jun 2020 09:15:57: 22000000 INFO @ Tue, 16 Jun 2020 09:16:00: 17000000 INFO @ Tue, 16 Jun 2020 09:16:00: 12000000 INFO @ Tue, 16 Jun 2020 09:16:03: 23000000 INFO @ Tue, 16 Jun 2020 09:16:06: 18000000 INFO @ Tue, 16 Jun 2020 09:16:06: 13000000 INFO @ Tue, 16 Jun 2020 09:16:09: 24000000 INFO @ Tue, 16 Jun 2020 09:16:11: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:16:11: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:16:11: #1 total tags in treatment: 11558981 INFO @ Tue, 16 Jun 2020 09:16:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:16:11: #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 09:16:11: #1 tags after filtering in treatment: 10215772 INFO @ Tue, 16 Jun 2020 09:16:11: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 16 Jun 2020 09:16:11: #1 finished! INFO @ Tue, 16 Jun 2020 09:16:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:16:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:16:11: #2 number of paired peaks: 249 WARNING @ Tue, 16 Jun 2020 09:16:11: Fewer paired peaks (249) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 249 pairs to build model! INFO @ Tue, 16 Jun 2020 09:16:11: start model_add_line... INFO @ Tue, 16 Jun 2020 09:16:12: start X-correlation... INFO @ Tue, 16 Jun 2020 09:16:12: end of X-cor INFO @ Tue, 16 Jun 2020 09:16:12: #2 finished! INFO @ Tue, 16 Jun 2020 09:16:12: #2 predicted fragment length is 106 bps INFO @ Tue, 16 Jun 2020 09:16:12: #2 alternative fragment length(s) may be 4,106,141 bps INFO @ Tue, 16 Jun 2020 09:16:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085348/SRX4085348.05_model.r INFO @ Tue, 16 Jun 2020 09:16:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:16:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:16:12: 19000000 INFO @ Tue, 16 Jun 2020 09:16:13: 14000000 INFO @ Tue, 16 Jun 2020 09:16:19: 20000000 INFO @ Tue, 16 Jun 2020 09:16:20: 15000000 INFO @ Tue, 16 Jun 2020 09:16:25: 21000000 INFO @ Tue, 16 Jun 2020 09:16:26: 16000000 INFO @ Tue, 16 Jun 2020 09:16:31: 22000000 INFO @ Tue, 16 Jun 2020 09:16:32: 17000000 INFO @ Tue, 16 Jun 2020 09:16:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:16:37: 23000000 INFO @ Tue, 16 Jun 2020 09:16:38: 18000000 INFO @ Tue, 16 Jun 2020 09:16:43: 24000000 INFO @ Tue, 16 Jun 2020 09:16:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085348/SRX4085348.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:16:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085348/SRX4085348.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:16:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085348/SRX4085348.05_summits.bed INFO @ Tue, 16 Jun 2020 09:16:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (609 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:16:45: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:16:45: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:16:45: #1 total tags in treatment: 11558981 INFO @ Tue, 16 Jun 2020 09:16:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:16:45: #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 09:16:45: 19000000 INFO @ Tue, 16 Jun 2020 09:16:45: #1 tags after filtering in treatment: 10215772 INFO @ Tue, 16 Jun 2020 09:16:45: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 16 Jun 2020 09:16:45: #1 finished! INFO @ Tue, 16 Jun 2020 09:16:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:16:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:16:45: #2 number of paired peaks: 249 WARNING @ Tue, 16 Jun 2020 09:16:45: Fewer paired peaks (249) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 249 pairs to build model! INFO @ Tue, 16 Jun 2020 09:16:45: start model_add_line... INFO @ Tue, 16 Jun 2020 09:16:46: start X-correlation... INFO @ Tue, 16 Jun 2020 09:16:46: end of X-cor INFO @ Tue, 16 Jun 2020 09:16:46: #2 finished! INFO @ Tue, 16 Jun 2020 09:16:46: #2 predicted fragment length is 106 bps INFO @ Tue, 16 Jun 2020 09:16:46: #2 alternative fragment length(s) may be 4,106,141 bps INFO @ Tue, 16 Jun 2020 09:16:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085348/SRX4085348.10_model.r INFO @ Tue, 16 Jun 2020 09:16:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:16:46: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:16:51: 20000000 INFO @ Tue, 16 Jun 2020 09:16:56: 21000000 INFO @ Tue, 16 Jun 2020 09:17:02: 22000000 INFO @ Tue, 16 Jun 2020 09:17:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:17:08: 23000000 INFO @ Tue, 16 Jun 2020 09:17:13: 24000000 INFO @ Tue, 16 Jun 2020 09:17:15: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:17:15: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:17:15: #1 total tags in treatment: 11558981 INFO @ Tue, 16 Jun 2020 09:17:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:17:15: #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 09:17:15: #1 tags after filtering in treatment: 10215772 INFO @ Tue, 16 Jun 2020 09:17:15: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 16 Jun 2020 09:17:15: #1 finished! INFO @ Tue, 16 Jun 2020 09:17:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:17:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:17:15: #2 number of paired peaks: 249 WARNING @ Tue, 16 Jun 2020 09:17:15: Fewer paired peaks (249) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 249 pairs to build model! INFO @ Tue, 16 Jun 2020 09:17:15: start model_add_line... INFO @ Tue, 16 Jun 2020 09:17:16: start X-correlation... INFO @ Tue, 16 Jun 2020 09:17:16: end of X-cor INFO @ Tue, 16 Jun 2020 09:17:16: #2 finished! INFO @ Tue, 16 Jun 2020 09:17:16: #2 predicted fragment length is 106 bps INFO @ Tue, 16 Jun 2020 09:17:16: #2 alternative fragment length(s) may be 4,106,141 bps INFO @ Tue, 16 Jun 2020 09:17:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085348/SRX4085348.20_model.r INFO @ Tue, 16 Jun 2020 09:17:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:17:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:17:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085348/SRX4085348.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:17:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085348/SRX4085348.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:17:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085348/SRX4085348.10_summits.bed INFO @ Tue, 16 Jun 2020 09:17:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (379 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:17:36: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:17:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085348/SRX4085348.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:17:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085348/SRX4085348.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:17:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085348/SRX4085348.20_summits.bed INFO @ Tue, 16 Jun 2020 09:17:46: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (199 records, 4 fields): 1 millis CompletedMACS2peakCalling