Job ID = 6367194 SRX = SRX2978698 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:30:05 prefetch.2.10.7: 1) Downloading 'SRR5799205'... 2020-06-15T23:30:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:34:08 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:34:08 prefetch.2.10.7: 1) 'SRR5799205' was downloaded successfully 2020-06-15T23:34:08 prefetch.2.10.7: 'SRR5799205' has 0 unresolved dependencies Read 18575859 spots for SRR5799205/SRR5799205.sra Written 18575859 spots for SRR5799205/SRR5799205.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: 00:21:25 18575859 reads; of these: 18575859 (100.00%) were paired; of these: 2863639 (15.42%) aligned concordantly 0 times 13211530 (71.12%) aligned concordantly exactly 1 time 2500690 (13.46%) aligned concordantly >1 times ---- 2863639 pairs aligned concordantly 0 times; of these: 1726103 (60.28%) aligned discordantly 1 time ---- 1137536 pairs aligned 0 times concordantly or discordantly; of these: 2275072 mates make up the pairs; of these: 1210978 (53.23%) aligned 0 times 608767 (26.76%) aligned exactly 1 time 455327 (20.01%) aligned >1 times 96.74% overall alignment rate Time searching: 00:21:25 Overall time: 00:21:25 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 16 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] 3280431 / 17429106 = 0.1882 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 09:08:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2978698/SRX2978698.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2978698/SRX2978698.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2978698/SRX2978698.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2978698/SRX2978698.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 09:08:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:08:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:08:56: 1000000 INFO @ Tue, 16 Jun 2020 09:09:02: 2000000 INFO @ Tue, 16 Jun 2020 09:09:09: 3000000 INFO @ Tue, 16 Jun 2020 09:09:15: 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 09:09:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2978698/SRX2978698.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2978698/SRX2978698.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2978698/SRX2978698.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2978698/SRX2978698.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 09:09:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:22: 5000000 INFO @ Tue, 16 Jun 2020 09:09:26: 1000000 INFO @ Tue, 16 Jun 2020 09:09:29: 6000000 INFO @ Tue, 16 Jun 2020 09:09:32: 2000000 INFO @ Tue, 16 Jun 2020 09:09:36: 7000000 INFO @ Tue, 16 Jun 2020 09:09:39: 3000000 INFO @ Tue, 16 Jun 2020 09:09:42: 8000000 INFO @ Tue, 16 Jun 2020 09:09:46: 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 09:09:49: 9000000 INFO @ Tue, 16 Jun 2020 09:09:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2978698/SRX2978698.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2978698/SRX2978698.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2978698/SRX2978698.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2978698/SRX2978698.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 09:09:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:52: 5000000 INFO @ Tue, 16 Jun 2020 09:09:55: 10000000 INFO @ Tue, 16 Jun 2020 09:09:56: 1000000 INFO @ Tue, 16 Jun 2020 09:09:58: 6000000 INFO @ Tue, 16 Jun 2020 09:10:02: 11000000 INFO @ Tue, 16 Jun 2020 09:10:03: 2000000 INFO @ Tue, 16 Jun 2020 09:10:05: 7000000 INFO @ Tue, 16 Jun 2020 09:10:09: 12000000 INFO @ Tue, 16 Jun 2020 09:10:09: 3000000 INFO @ Tue, 16 Jun 2020 09:10:13: 8000000 INFO @ Tue, 16 Jun 2020 09:10:16: 13000000 INFO @ Tue, 16 Jun 2020 09:10:16: 4000000 INFO @ Tue, 16 Jun 2020 09:10:20: 9000000 INFO @ Tue, 16 Jun 2020 09:10:23: 5000000 INFO @ Tue, 16 Jun 2020 09:10:23: 14000000 INFO @ Tue, 16 Jun 2020 09:10:27: 10000000 INFO @ Tue, 16 Jun 2020 09:10:30: 6000000 INFO @ Tue, 16 Jun 2020 09:10:30: 15000000 INFO @ Tue, 16 Jun 2020 09:10:34: 11000000 INFO @ Tue, 16 Jun 2020 09:10:37: 7000000 INFO @ Tue, 16 Jun 2020 09:10:37: 16000000 INFO @ Tue, 16 Jun 2020 09:10:41: 12000000 INFO @ Tue, 16 Jun 2020 09:10:43: 8000000 INFO @ Tue, 16 Jun 2020 09:10:43: 17000000 INFO @ Tue, 16 Jun 2020 09:10:47: 13000000 INFO @ Tue, 16 Jun 2020 09:10:49: 9000000 INFO @ Tue, 16 Jun 2020 09:10:49: 18000000 INFO @ Tue, 16 Jun 2020 09:10:54: 14000000 INFO @ Tue, 16 Jun 2020 09:10:55: 10000000 INFO @ Tue, 16 Jun 2020 09:10:56: 19000000 INFO @ Tue, 16 Jun 2020 09:11:00: 15000000 INFO @ Tue, 16 Jun 2020 09:11:02: 11000000 INFO @ Tue, 16 Jun 2020 09:11:02: 20000000 INFO @ Tue, 16 Jun 2020 09:11:06: 16000000 INFO @ Tue, 16 Jun 2020 09:11:08: 21000000 INFO @ Tue, 16 Jun 2020 09:11:08: 12000000 INFO @ Tue, 16 Jun 2020 09:11:13: 17000000 INFO @ Tue, 16 Jun 2020 09:11:15: 22000000 INFO @ Tue, 16 Jun 2020 09:11:15: 13000000 INFO @ Tue, 16 Jun 2020 09:11:20: 18000000 INFO @ Tue, 16 Jun 2020 09:11:22: 23000000 INFO @ Tue, 16 Jun 2020 09:11:22: 14000000 INFO @ Tue, 16 Jun 2020 09:11:26: 19000000 INFO @ Tue, 16 Jun 2020 09:11:28: 24000000 INFO @ Tue, 16 Jun 2020 09:11:28: 15000000 INFO @ Tue, 16 Jun 2020 09:11:32: 20000000 INFO @ Tue, 16 Jun 2020 09:11:34: 25000000 INFO @ Tue, 16 Jun 2020 09:11:35: 16000000 INFO @ Tue, 16 Jun 2020 09:11:38: 21000000 INFO @ Tue, 16 Jun 2020 09:11:40: 26000000 INFO @ Tue, 16 Jun 2020 09:11:41: 17000000 INFO @ Tue, 16 Jun 2020 09:11:44: 22000000 INFO @ Tue, 16 Jun 2020 09:11:47: 27000000 INFO @ Tue, 16 Jun 2020 09:11:47: 18000000 INFO @ Tue, 16 Jun 2020 09:11:51: 23000000 INFO @ Tue, 16 Jun 2020 09:11:53: 28000000 INFO @ Tue, 16 Jun 2020 09:11:53: 19000000 INFO @ Tue, 16 Jun 2020 09:11:57: 24000000 INFO @ Tue, 16 Jun 2020 09:11:59: 29000000 INFO @ Tue, 16 Jun 2020 09:11:59: 20000000 INFO @ Tue, 16 Jun 2020 09:12:02: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:12:02: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:12:02: #1 total tags in treatment: 12571900 INFO @ Tue, 16 Jun 2020 09:12:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:02: #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 09:12:02: #1 tags after filtering in treatment: 11479835 INFO @ Tue, 16 Jun 2020 09:12:02: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 16 Jun 2020 09:12:02: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:03: 25000000 INFO @ Tue, 16 Jun 2020 09:12:03: #2 number of paired peaks: 495 WARNING @ Tue, 16 Jun 2020 09:12:03: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:03: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:03: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:03: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:03: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:03: #2 predicted fragment length is 144 bps INFO @ Tue, 16 Jun 2020 09:12:03: #2 alternative fragment length(s) may be 4,144 bps INFO @ Tue, 16 Jun 2020 09:12:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2978698/SRX2978698.05_model.r INFO @ Tue, 16 Jun 2020 09:12:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:05: 21000000 INFO @ Tue, 16 Jun 2020 09:12:08: 26000000 INFO @ Tue, 16 Jun 2020 09:12:11: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:12:14: 27000000 INFO @ Tue, 16 Jun 2020 09:12:17: 23000000 INFO @ Tue, 16 Jun 2020 09:12:20: 28000000 INFO @ Tue, 16 Jun 2020 09:12:22: 24000000 INFO @ Tue, 16 Jun 2020 09:12:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:26: 29000000 INFO @ Tue, 16 Jun 2020 09:12:28: 25000000 INFO @ Tue, 16 Jun 2020 09:12:28: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:12:28: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:12:28: #1 total tags in treatment: 12571900 INFO @ Tue, 16 Jun 2020 09:12:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:28: #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 09:12:29: #1 tags after filtering in treatment: 11479835 INFO @ Tue, 16 Jun 2020 09:12:29: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 16 Jun 2020 09:12:29: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:29: #2 number of paired peaks: 495 WARNING @ Tue, 16 Jun 2020 09:12:29: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:29: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:30: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:30: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:30: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:30: #2 predicted fragment length is 144 bps INFO @ Tue, 16 Jun 2020 09:12:30: #2 alternative fragment length(s) may be 4,144 bps INFO @ Tue, 16 Jun 2020 09:12:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2978698/SRX2978698.10_model.r INFO @ Tue, 16 Jun 2020 09:12:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:35: 26000000 INFO @ Tue, 16 Jun 2020 09:12:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2978698/SRX2978698.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2978698/SRX2978698.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2978698/SRX2978698.05_summits.bed INFO @ Tue, 16 Jun 2020 09:12:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (442 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:12:41: 27000000 INFO @ Tue, 16 Jun 2020 09:12:47: 28000000 INFO @ Tue, 16 Jun 2020 09:12:52: 29000000 INFO @ Tue, 16 Jun 2020 09:12:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:54: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:12:54: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:12:54: #1 total tags in treatment: 12571900 INFO @ Tue, 16 Jun 2020 09:12:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:54: #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 09:12:55: #1 tags after filtering in treatment: 11479835 INFO @ Tue, 16 Jun 2020 09:12:55: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 16 Jun 2020 09:12:55: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:55: #2 number of paired peaks: 495 WARNING @ Tue, 16 Jun 2020 09:12:55: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:55: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:56: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:56: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:56: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:56: #2 predicted fragment length is 144 bps INFO @ Tue, 16 Jun 2020 09:12:56: #2 alternative fragment length(s) may be 4,144 bps INFO @ Tue, 16 Jun 2020 09:12:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2978698/SRX2978698.20_model.r INFO @ Tue, 16 Jun 2020 09:12:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:13:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2978698/SRX2978698.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:13:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2978698/SRX2978698.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:13:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2978698/SRX2978698.10_summits.bed INFO @ Tue, 16 Jun 2020 09:13:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (330 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:13:18: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:13:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2978698/SRX2978698.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:13:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2978698/SRX2978698.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:13:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2978698/SRX2978698.20_summits.bed INFO @ Tue, 16 Jun 2020 09:13:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (226 records, 4 fields): 1 millis CompletedMACS2peakCalling