Job ID = 6368447 SRX = SRX4996803 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-16T00:26:01 prefetch.2.10.7: 1) Downloading 'SRR8176688'... 2020-06-16T00:26:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:29:36 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:29:36 prefetch.2.10.7: 1) 'SRR8176688' was downloaded successfully 2020-06-16T00:29:36 prefetch.2.10.7: 'SRR8176688' has 0 unresolved dependencies Read 21341230 spots for SRR8176688/SRR8176688.sra Written 21341230 spots for SRR8176688/SRR8176688.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: 00:20:31 21341230 reads; of these: 21341230 (100.00%) were paired; of these: 1594009 (7.47%) aligned concordantly 0 times 15978431 (74.87%) aligned concordantly exactly 1 time 3768790 (17.66%) aligned concordantly >1 times ---- 1594009 pairs aligned concordantly 0 times; of these: 814224 (51.08%) aligned discordantly 1 time ---- 779785 pairs aligned 0 times concordantly or discordantly; of these: 1559570 mates make up the pairs; of these: 784380 (50.29%) aligned 0 times 424845 (27.24%) aligned exactly 1 time 350345 (22.46%) aligned >1 times 98.16% overall alignment rate Time searching: 00:20:31 Overall time: 00:20:31 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 20 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] 1963717 / 20531429 = 0.0956 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 10:01:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4996803/SRX4996803.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4996803/SRX4996803.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4996803/SRX4996803.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4996803/SRX4996803.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 10:01:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:01:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:01:53: 1000000 INFO @ Tue, 16 Jun 2020 10:01:58: 2000000 INFO @ Tue, 16 Jun 2020 10:02:03: 3000000 INFO @ Tue, 16 Jun 2020 10:02:08: 4000000 INFO @ Tue, 16 Jun 2020 10:02:12: 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 @ Tue, 16 Jun 2020 10:02:17: 6000000 INFO @ Tue, 16 Jun 2020 10:02:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4996803/SRX4996803.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4996803/SRX4996803.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4996803/SRX4996803.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4996803/SRX4996803.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 10:02:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:02:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:02:22: 7000000 INFO @ Tue, 16 Jun 2020 10:02:24: 1000000 INFO @ Tue, 16 Jun 2020 10:02:27: 8000000 INFO @ Tue, 16 Jun 2020 10:02:29: 2000000 INFO @ Tue, 16 Jun 2020 10:02:33: 9000000 INFO @ Tue, 16 Jun 2020 10:02:34: 3000000 INFO @ Tue, 16 Jun 2020 10:02:38: 10000000 INFO @ Tue, 16 Jun 2020 10:02:40: 4000000 INFO @ Tue, 16 Jun 2020 10:02:43: 11000000 INFO @ Tue, 16 Jun 2020 10:02:45: 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 @ Tue, 16 Jun 2020 10:02:49: 12000000 INFO @ Tue, 16 Jun 2020 10:02:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4996803/SRX4996803.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4996803/SRX4996803.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4996803/SRX4996803.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4996803/SRX4996803.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 10:02:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:02:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:02:50: 6000000 INFO @ Tue, 16 Jun 2020 10:02:54: 13000000 INFO @ Tue, 16 Jun 2020 10:02:54: 1000000 INFO @ Tue, 16 Jun 2020 10:02:55: 7000000 INFO @ Tue, 16 Jun 2020 10:02:59: 2000000 INFO @ Tue, 16 Jun 2020 10:02:59: 14000000 INFO @ Tue, 16 Jun 2020 10:03:00: 8000000 INFO @ Tue, 16 Jun 2020 10:03:04: 3000000 INFO @ Tue, 16 Jun 2020 10:03:05: 15000000 INFO @ Tue, 16 Jun 2020 10:03:05: 9000000 INFO @ Tue, 16 Jun 2020 10:03:10: 4000000 INFO @ Tue, 16 Jun 2020 10:03:10: 16000000 INFO @ Tue, 16 Jun 2020 10:03:11: 10000000 INFO @ Tue, 16 Jun 2020 10:03:15: 5000000 INFO @ Tue, 16 Jun 2020 10:03:15: 17000000 INFO @ Tue, 16 Jun 2020 10:03:16: 11000000 INFO @ Tue, 16 Jun 2020 10:03:20: 6000000 INFO @ Tue, 16 Jun 2020 10:03:20: 18000000 INFO @ Tue, 16 Jun 2020 10:03:21: 12000000 INFO @ Tue, 16 Jun 2020 10:03:25: 7000000 INFO @ Tue, 16 Jun 2020 10:03:25: 19000000 INFO @ Tue, 16 Jun 2020 10:03:26: 13000000 INFO @ Tue, 16 Jun 2020 10:03:30: 8000000 INFO @ Tue, 16 Jun 2020 10:03:30: 20000000 INFO @ Tue, 16 Jun 2020 10:03:31: 14000000 INFO @ Tue, 16 Jun 2020 10:03:35: 9000000 INFO @ Tue, 16 Jun 2020 10:03:36: 21000000 INFO @ Tue, 16 Jun 2020 10:03:36: 15000000 INFO @ Tue, 16 Jun 2020 10:03:40: 10000000 INFO @ Tue, 16 Jun 2020 10:03:41: 22000000 INFO @ Tue, 16 Jun 2020 10:03:42: 16000000 INFO @ Tue, 16 Jun 2020 10:03:46: 11000000 INFO @ Tue, 16 Jun 2020 10:03:46: 23000000 INFO @ Tue, 16 Jun 2020 10:03:47: 17000000 INFO @ Tue, 16 Jun 2020 10:03:51: 12000000 INFO @ Tue, 16 Jun 2020 10:03:51: 24000000 INFO @ Tue, 16 Jun 2020 10:03:52: 18000000 INFO @ Tue, 16 Jun 2020 10:03:56: 13000000 INFO @ Tue, 16 Jun 2020 10:03:56: 25000000 INFO @ Tue, 16 Jun 2020 10:03:57: 19000000 INFO @ Tue, 16 Jun 2020 10:04:01: 14000000 INFO @ Tue, 16 Jun 2020 10:04:01: 26000000 INFO @ Tue, 16 Jun 2020 10:04:02: 20000000 INFO @ Tue, 16 Jun 2020 10:04:06: 15000000 INFO @ Tue, 16 Jun 2020 10:04:06: 27000000 INFO @ Tue, 16 Jun 2020 10:04:07: 21000000 INFO @ Tue, 16 Jun 2020 10:04:11: 16000000 INFO @ Tue, 16 Jun 2020 10:04:11: 28000000 INFO @ Tue, 16 Jun 2020 10:04:12: 22000000 INFO @ Tue, 16 Jun 2020 10:04:16: 17000000 INFO @ Tue, 16 Jun 2020 10:04:16: 29000000 INFO @ Tue, 16 Jun 2020 10:04:17: 23000000 INFO @ Tue, 16 Jun 2020 10:04:21: 18000000 INFO @ Tue, 16 Jun 2020 10:04:21: 30000000 INFO @ Tue, 16 Jun 2020 10:04:22: 24000000 INFO @ Tue, 16 Jun 2020 10:04:26: 19000000 INFO @ Tue, 16 Jun 2020 10:04:26: 31000000 INFO @ Tue, 16 Jun 2020 10:04:27: 25000000 INFO @ Tue, 16 Jun 2020 10:04:31: 20000000 INFO @ Tue, 16 Jun 2020 10:04:31: 32000000 INFO @ Tue, 16 Jun 2020 10:04:32: 26000000 INFO @ Tue, 16 Jun 2020 10:04:36: 21000000 INFO @ Tue, 16 Jun 2020 10:04:36: 33000000 INFO @ Tue, 16 Jun 2020 10:04:37: 27000000 INFO @ Tue, 16 Jun 2020 10:04:41: 22000000 INFO @ Tue, 16 Jun 2020 10:04:41: 34000000 INFO @ Tue, 16 Jun 2020 10:04:42: 28000000 INFO @ Tue, 16 Jun 2020 10:04:46: 23000000 INFO @ Tue, 16 Jun 2020 10:04:47: 35000000 INFO @ Tue, 16 Jun 2020 10:04:47: 29000000 INFO @ Tue, 16 Jun 2020 10:04:51: 24000000 INFO @ Tue, 16 Jun 2020 10:04:52: 36000000 INFO @ Tue, 16 Jun 2020 10:04:53: 30000000 INFO @ Tue, 16 Jun 2020 10:04:56: 25000000 INFO @ Tue, 16 Jun 2020 10:04:57: 37000000 INFO @ Tue, 16 Jun 2020 10:04:58: 31000000 INFO @ Tue, 16 Jun 2020 10:05:02: 26000000 INFO @ Tue, 16 Jun 2020 10:05:02: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 10:05:02: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 10:05:02: #1 total tags in treatment: 17811521 INFO @ Tue, 16 Jun 2020 10:05:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:05:02: #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 10:05:03: #1 tags after filtering in treatment: 15660844 INFO @ Tue, 16 Jun 2020 10:05:03: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 16 Jun 2020 10:05:03: #1 finished! INFO @ Tue, 16 Jun 2020 10:05:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:05:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:05:03: 32000000 INFO @ Tue, 16 Jun 2020 10:05:04: #2 number of paired peaks: 434 WARNING @ Tue, 16 Jun 2020 10:05:04: Fewer paired peaks (434) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 434 pairs to build model! INFO @ Tue, 16 Jun 2020 10:05:04: start model_add_line... INFO @ Tue, 16 Jun 2020 10:05:04: start X-correlation... INFO @ Tue, 16 Jun 2020 10:05:04: end of X-cor INFO @ Tue, 16 Jun 2020 10:05:04: #2 finished! INFO @ Tue, 16 Jun 2020 10:05:04: #2 predicted fragment length is 126 bps INFO @ Tue, 16 Jun 2020 10:05:04: #2 alternative fragment length(s) may be 3,126 bps INFO @ Tue, 16 Jun 2020 10:05:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4996803/SRX4996803.05_model.r INFO @ Tue, 16 Jun 2020 10:05:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:05:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:05:07: 27000000 INFO @ Tue, 16 Jun 2020 10:05:08: 33000000 INFO @ Tue, 16 Jun 2020 10:05:12: 28000000 INFO @ Tue, 16 Jun 2020 10:05:13: 34000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:05:17: 29000000 INFO @ Tue, 16 Jun 2020 10:05:19: 35000000 INFO @ Tue, 16 Jun 2020 10:05:23: 30000000 INFO @ Tue, 16 Jun 2020 10:05:24: 36000000 INFO @ Tue, 16 Jun 2020 10:05:28: 31000000 INFO @ Tue, 16 Jun 2020 10:05:29: 37000000 INFO @ Tue, 16 Jun 2020 10:05:33: 32000000 INFO @ Tue, 16 Jun 2020 10:05:35: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 10:05:35: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 10:05:35: #1 total tags in treatment: 17811521 INFO @ Tue, 16 Jun 2020 10:05:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:05:35: #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 10:05:35: #1 tags after filtering in treatment: 15660844 INFO @ Tue, 16 Jun 2020 10:05:35: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 16 Jun 2020 10:05:35: #1 finished! INFO @ Tue, 16 Jun 2020 10:05:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:05:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:05:36: #2 number of paired peaks: 434 WARNING @ Tue, 16 Jun 2020 10:05:36: Fewer paired peaks (434) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 434 pairs to build model! INFO @ Tue, 16 Jun 2020 10:05:36: start model_add_line... INFO @ Tue, 16 Jun 2020 10:05:36: start X-correlation... INFO @ Tue, 16 Jun 2020 10:05:36: end of X-cor INFO @ Tue, 16 Jun 2020 10:05:36: #2 finished! INFO @ Tue, 16 Jun 2020 10:05:36: #2 predicted fragment length is 126 bps INFO @ Tue, 16 Jun 2020 10:05:36: #2 alternative fragment length(s) may be 3,126 bps INFO @ Tue, 16 Jun 2020 10:05:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4996803/SRX4996803.10_model.r INFO @ Tue, 16 Jun 2020 10:05:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:05:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:05:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:05:38: 33000000 INFO @ Tue, 16 Jun 2020 10:05:43: 34000000 INFO @ Tue, 16 Jun 2020 10:05:48: 35000000 INFO @ Tue, 16 Jun 2020 10:05:54: 36000000 INFO @ Tue, 16 Jun 2020 10:05:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4996803/SRX4996803.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:05:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4996803/SRX4996803.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:05:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4996803/SRX4996803.05_summits.bed INFO @ Tue, 16 Jun 2020 10:05:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (465 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:05:59: 37000000 INFO @ Tue, 16 Jun 2020 10:06:04: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 10:06:04: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 10:06:04: #1 total tags in treatment: 17811521 INFO @ Tue, 16 Jun 2020 10:06:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:06:04: #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 10:06:04: #1 tags after filtering in treatment: 15660844 INFO @ Tue, 16 Jun 2020 10:06:04: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 16 Jun 2020 10:06:04: #1 finished! INFO @ Tue, 16 Jun 2020 10:06:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:06:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:06:05: #2 number of paired peaks: 434 WARNING @ Tue, 16 Jun 2020 10:06:05: Fewer paired peaks (434) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 434 pairs to build model! INFO @ Tue, 16 Jun 2020 10:06:05: start model_add_line... INFO @ Tue, 16 Jun 2020 10:06:05: start X-correlation... INFO @ Tue, 16 Jun 2020 10:06:05: end of X-cor INFO @ Tue, 16 Jun 2020 10:06:05: #2 finished! INFO @ Tue, 16 Jun 2020 10:06:05: #2 predicted fragment length is 126 bps INFO @ Tue, 16 Jun 2020 10:06:05: #2 alternative fragment length(s) may be 3,126 bps INFO @ Tue, 16 Jun 2020 10:06:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4996803/SRX4996803.20_model.r INFO @ Tue, 16 Jun 2020 10:06:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:06:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:06:10: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:06:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4996803/SRX4996803.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:06:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4996803/SRX4996803.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:06:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4996803/SRX4996803.10_summits.bed INFO @ Tue, 16 Jun 2020 10:06:27: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (347 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:06:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:06:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4996803/SRX4996803.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:06:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4996803/SRX4996803.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:06:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4996803/SRX4996803.20_summits.bed INFO @ Tue, 16 Jun 2020 10:06:54: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (234 records, 4 fields): 2 millis CompletedMACS2peakCalling