Job ID = 6507767 SRX = SRX4085354 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T13:21:04 prefetch.2.10.7: 1) Downloading 'SRR7167383'... 2020-06-26T13:21:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:29:00 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:29:00 prefetch.2.10.7: 1) 'SRR7167383' was downloaded successfully Read 40640884 spots for SRR7167383/SRR7167383.sra Written 40640884 spots for SRR7167383/SRR7167383.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: 00:32:11 40640884 reads; of these: 40640884 (100.00%) were paired; of these: 3657571 (9.00%) aligned concordantly 0 times 32896868 (80.95%) aligned concordantly exactly 1 time 4086445 (10.06%) aligned concordantly >1 times ---- 3657571 pairs aligned concordantly 0 times; of these: 496666 (13.58%) aligned discordantly 1 time ---- 3160905 pairs aligned 0 times concordantly or discordantly; of these: 6321810 mates make up the pairs; of these: 4215564 (66.68%) aligned 0 times 1658619 (26.24%) aligned exactly 1 time 447627 (7.08%) aligned >1 times 94.81% overall alignment rate Time searching: 00:32:11 Overall time: 00:32:11 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 32 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] 23984004 / 37264735 = 0.6436 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 23:21:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085354/SRX4085354.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085354/SRX4085354.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085354/SRX4085354.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085354/SRX4085354.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 23:21:38: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:21:38: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:21:43: 1000000 INFO @ Fri, 26 Jun 2020 23:21:48: 2000000 INFO @ Fri, 26 Jun 2020 23:21:53: 3000000 INFO @ Fri, 26 Jun 2020 23:21:58: 4000000 INFO @ Fri, 26 Jun 2020 23:22:03: 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 @ Fri, 26 Jun 2020 23:22:08: 6000000 INFO @ Fri, 26 Jun 2020 23:22:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085354/SRX4085354.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085354/SRX4085354.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085354/SRX4085354.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085354/SRX4085354.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 23:22:08: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:22:08: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:22:14: 7000000 INFO @ Fri, 26 Jun 2020 23:22:14: 1000000 INFO @ Fri, 26 Jun 2020 23:22:19: 8000000 INFO @ Fri, 26 Jun 2020 23:22:19: 2000000 INFO @ Fri, 26 Jun 2020 23:22:24: 9000000 INFO @ Fri, 26 Jun 2020 23:22:25: 3000000 INFO @ Fri, 26 Jun 2020 23:22:30: 10000000 INFO @ Fri, 26 Jun 2020 23:22:30: 4000000 INFO @ Fri, 26 Jun 2020 23:22:35: 11000000 INFO @ Fri, 26 Jun 2020 23:22:35: 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 @ Fri, 26 Jun 2020 23:22:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085354/SRX4085354.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085354/SRX4085354.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085354/SRX4085354.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085354/SRX4085354.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 23:22:38: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:22:38: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:22:41: 12000000 INFO @ Fri, 26 Jun 2020 23:22:41: 6000000 INFO @ Fri, 26 Jun 2020 23:22:44: 1000000 INFO @ Fri, 26 Jun 2020 23:22:47: 13000000 INFO @ Fri, 26 Jun 2020 23:22:47: 7000000 INFO @ Fri, 26 Jun 2020 23:22:50: 2000000 INFO @ Fri, 26 Jun 2020 23:22:52: 14000000 INFO @ Fri, 26 Jun 2020 23:22:53: 8000000 INFO @ Fri, 26 Jun 2020 23:22:57: 3000000 INFO @ Fri, 26 Jun 2020 23:22:58: 15000000 INFO @ Fri, 26 Jun 2020 23:22:58: 9000000 INFO @ Fri, 26 Jun 2020 23:23:03: 4000000 INFO @ Fri, 26 Jun 2020 23:23:04: 16000000 INFO @ Fri, 26 Jun 2020 23:23:04: 10000000 INFO @ Fri, 26 Jun 2020 23:23:09: 5000000 INFO @ Fri, 26 Jun 2020 23:23:10: 17000000 INFO @ Fri, 26 Jun 2020 23:23:10: 11000000 INFO @ Fri, 26 Jun 2020 23:23:16: 18000000 INFO @ Fri, 26 Jun 2020 23:23:16: 6000000 INFO @ Fri, 26 Jun 2020 23:23:16: 12000000 INFO @ Fri, 26 Jun 2020 23:23:21: 19000000 INFO @ Fri, 26 Jun 2020 23:23:21: 13000000 INFO @ Fri, 26 Jun 2020 23:23:22: 7000000 INFO @ Fri, 26 Jun 2020 23:23:27: 20000000 INFO @ Fri, 26 Jun 2020 23:23:27: 14000000 INFO @ Fri, 26 Jun 2020 23:23:28: 8000000 INFO @ Fri, 26 Jun 2020 23:23:33: 21000000 INFO @ Fri, 26 Jun 2020 23:23:33: 15000000 INFO @ Fri, 26 Jun 2020 23:23:35: 9000000 INFO @ Fri, 26 Jun 2020 23:23:39: 22000000 INFO @ Fri, 26 Jun 2020 23:23:39: 16000000 INFO @ Fri, 26 Jun 2020 23:23:41: 10000000 INFO @ Fri, 26 Jun 2020 23:23:45: 17000000 INFO @ Fri, 26 Jun 2020 23:23:45: 23000000 INFO @ Fri, 26 Jun 2020 23:23:48: 11000000 INFO @ Fri, 26 Jun 2020 23:23:50: 24000000 INFO @ Fri, 26 Jun 2020 23:23:50: 18000000 INFO @ Fri, 26 Jun 2020 23:23:54: 12000000 INFO @ Fri, 26 Jun 2020 23:23:56: 19000000 INFO @ Fri, 26 Jun 2020 23:23:56: 25000000 INFO @ Fri, 26 Jun 2020 23:24:00: 13000000 INFO @ Fri, 26 Jun 2020 23:24:02: 20000000 INFO @ Fri, 26 Jun 2020 23:24:02: 26000000 INFO @ Fri, 26 Jun 2020 23:24:06: 14000000 INFO @ Fri, 26 Jun 2020 23:24:08: 27000000 INFO @ Fri, 26 Jun 2020 23:24:08: 21000000 INFO @ Fri, 26 Jun 2020 23:24:12: 15000000 INFO @ Fri, 26 Jun 2020 23:24:13: 28000000 INFO @ Fri, 26 Jun 2020 23:24:13: 22000000 INFO @ Fri, 26 Jun 2020 23:24:18: 16000000 INFO @ Fri, 26 Jun 2020 23:24:19: 29000000 INFO @ Fri, 26 Jun 2020 23:24:19: 23000000 INFO @ Fri, 26 Jun 2020 23:24:20: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 23:24:20: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 23:24:20: #1 total tags in treatment: 13155399 INFO @ Fri, 26 Jun 2020 23:24:20: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:24:20: #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 23:24:20: #1 tags after filtering in treatment: 11614986 INFO @ Fri, 26 Jun 2020 23:24:20: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 26 Jun 2020 23:24:20: #1 finished! INFO @ Fri, 26 Jun 2020 23:24:20: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:24:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:24:21: #2 number of paired peaks: 259 WARNING @ Fri, 26 Jun 2020 23:24:21: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Fri, 26 Jun 2020 23:24:21: start model_add_line... INFO @ Fri, 26 Jun 2020 23:24:21: start X-correlation... INFO @ Fri, 26 Jun 2020 23:24:21: end of X-cor INFO @ Fri, 26 Jun 2020 23:24:21: #2 finished! INFO @ Fri, 26 Jun 2020 23:24:21: #2 predicted fragment length is 104 bps INFO @ Fri, 26 Jun 2020 23:24:21: #2 alternative fragment length(s) may be 3,104,117,176,188 bps INFO @ Fri, 26 Jun 2020 23:24:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085354/SRX4085354.05_model.r INFO @ Fri, 26 Jun 2020 23:24:21: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:24:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:24:24: 17000000 INFO @ Fri, 26 Jun 2020 23:24:25: 24000000 INFO @ Fri, 26 Jun 2020 23:24:30: 18000000 INFO @ Fri, 26 Jun 2020 23:24:30: 25000000 INFO @ Fri, 26 Jun 2020 23:24:36: 26000000 INFO @ Fri, 26 Jun 2020 23:24:36: 19000000 INFO @ Fri, 26 Jun 2020 23:24:41: 27000000 INFO @ Fri, 26 Jun 2020 23:24:42: 20000000 INFO @ Fri, 26 Jun 2020 23:24:46: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:24:47: 28000000 INFO @ Fri, 26 Jun 2020 23:24:48: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:24:52: 29000000 INFO @ Fri, 26 Jun 2020 23:24:53: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 23:24:53: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 23:24:53: #1 total tags in treatment: 13155399 INFO @ Fri, 26 Jun 2020 23:24:53: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:24:53: #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 23:24:53: #1 tags after filtering in treatment: 11614986 INFO @ Fri, 26 Jun 2020 23:24:53: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 26 Jun 2020 23:24:53: #1 finished! INFO @ Fri, 26 Jun 2020 23:24:53: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:24:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:24:54: 22000000 INFO @ Fri, 26 Jun 2020 23:24:54: #2 number of paired peaks: 259 WARNING @ Fri, 26 Jun 2020 23:24:54: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Fri, 26 Jun 2020 23:24:54: start model_add_line... INFO @ Fri, 26 Jun 2020 23:24:54: start X-correlation... INFO @ Fri, 26 Jun 2020 23:24:54: end of X-cor INFO @ Fri, 26 Jun 2020 23:24:54: #2 finished! INFO @ Fri, 26 Jun 2020 23:24:54: #2 predicted fragment length is 104 bps INFO @ Fri, 26 Jun 2020 23:24:54: #2 alternative fragment length(s) may be 3,104,117,176,188 bps INFO @ Fri, 26 Jun 2020 23:24:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085354/SRX4085354.10_model.r INFO @ Fri, 26 Jun 2020 23:24:54: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:24:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:24:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085354/SRX4085354.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:24:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085354/SRX4085354.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:24:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085354/SRX4085354.05_summits.bed INFO @ Fri, 26 Jun 2020 23:24:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (434 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:25:00: 23000000 INFO @ Fri, 26 Jun 2020 23:25:06: 24000000 INFO @ Fri, 26 Jun 2020 23:25:12: 25000000 INFO @ Fri, 26 Jun 2020 23:25:18: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:25:18: 26000000 INFO @ Fri, 26 Jun 2020 23:25:23: 27000000 INFO @ Fri, 26 Jun 2020 23:25:29: 28000000 INFO @ Fri, 26 Jun 2020 23:25:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085354/SRX4085354.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:25:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085354/SRX4085354.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:25:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085354/SRX4085354.10_summits.bed INFO @ Fri, 26 Jun 2020 23:25:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (277 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:25:35: 29000000 INFO @ Fri, 26 Jun 2020 23:25:35: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 23:25:35: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 23:25:35: #1 total tags in treatment: 13155399 INFO @ Fri, 26 Jun 2020 23:25:35: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:25:35: #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 23:25:36: #1 tags after filtering in treatment: 11614986 INFO @ Fri, 26 Jun 2020 23:25:36: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 26 Jun 2020 23:25:36: #1 finished! INFO @ Fri, 26 Jun 2020 23:25:36: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:25:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:25:36: #2 number of paired peaks: 259 WARNING @ Fri, 26 Jun 2020 23:25:36: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Fri, 26 Jun 2020 23:25:36: start model_add_line... INFO @ Fri, 26 Jun 2020 23:25:36: start X-correlation... INFO @ Fri, 26 Jun 2020 23:25:36: end of X-cor INFO @ Fri, 26 Jun 2020 23:25:36: #2 finished! INFO @ Fri, 26 Jun 2020 23:25:36: #2 predicted fragment length is 104 bps INFO @ Fri, 26 Jun 2020 23:25:36: #2 alternative fragment length(s) may be 3,104,117,176,188 bps INFO @ Fri, 26 Jun 2020 23:25:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085354/SRX4085354.20_model.r INFO @ Fri, 26 Jun 2020 23:25:36: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:25:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:26:01: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:26:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085354/SRX4085354.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:26:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085354/SRX4085354.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:26:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085354/SRX4085354.20_summits.bed INFO @ Fri, 26 Jun 2020 23:26:13: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (152 records, 4 fields): 2 millis CompletedMACS2peakCalling