Job ID = 6368464 SRX = SRX4996821 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-16T00:18:36 prefetch.2.10.7: 1) Downloading 'SRR8176706'... 2020-06-16T00:18:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:22:31 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:22:31 prefetch.2.10.7: 1) 'SRR8176706' was downloaded successfully 2020-06-16T00:22:31 prefetch.2.10.7: 'SRR8176706' has 0 unresolved dependencies Read 21208238 spots for SRR8176706/SRR8176706.sra Written 21208238 spots for SRR8176706/SRR8176706.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: 00:17:53 21208238 reads; of these: 21208238 (100.00%) were paired; of these: 2005648 (9.46%) aligned concordantly 0 times 16405946 (77.36%) aligned concordantly exactly 1 time 2796644 (13.19%) aligned concordantly >1 times ---- 2005648 pairs aligned concordantly 0 times; of these: 1425403 (71.07%) aligned discordantly 1 time ---- 580245 pairs aligned 0 times concordantly or discordantly; of these: 1160490 mates make up the pairs; of these: 474407 (40.88%) aligned 0 times 331668 (28.58%) aligned exactly 1 time 354415 (30.54%) aligned >1 times 98.88% overall alignment rate Time searching: 00:17:53 Overall time: 00:17:53 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] 246714 / 20612816 = 0.0120 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 09:52:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4996821/SRX4996821.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4996821/SRX4996821.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4996821/SRX4996821.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4996821/SRX4996821.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 09:52:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:52:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:52:14: 1000000 INFO @ Tue, 16 Jun 2020 09:52:19: 2000000 INFO @ Tue, 16 Jun 2020 09:52:24: 3000000 INFO @ Tue, 16 Jun 2020 09:52:29: 4000000 INFO @ Tue, 16 Jun 2020 09:52:33: 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 09:52:38: 6000000 INFO @ Tue, 16 Jun 2020 09:52:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4996821/SRX4996821.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4996821/SRX4996821.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4996821/SRX4996821.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4996821/SRX4996821.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 09:52:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:52:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:52:43: 7000000 INFO @ Tue, 16 Jun 2020 09:52:44: 1000000 INFO @ Tue, 16 Jun 2020 09:52:49: 8000000 INFO @ Tue, 16 Jun 2020 09:52:49: 2000000 INFO @ Tue, 16 Jun 2020 09:52:54: 9000000 INFO @ Tue, 16 Jun 2020 09:52:55: 3000000 INFO @ Tue, 16 Jun 2020 09:52:59: 10000000 INFO @ Tue, 16 Jun 2020 09:53:00: 4000000 INFO @ Tue, 16 Jun 2020 09:53:05: 11000000 INFO @ Tue, 16 Jun 2020 09:53:05: 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 09:53:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4996821/SRX4996821.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4996821/SRX4996821.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4996821/SRX4996821.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4996821/SRX4996821.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 09:53:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:53:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:53:10: 12000000 INFO @ Tue, 16 Jun 2020 09:53:11: 6000000 INFO @ Tue, 16 Jun 2020 09:53:15: 1000000 INFO @ Tue, 16 Jun 2020 09:53:16: 13000000 INFO @ Tue, 16 Jun 2020 09:53:17: 7000000 INFO @ Tue, 16 Jun 2020 09:53:22: 14000000 INFO @ Tue, 16 Jun 2020 09:53:22: 2000000 INFO @ Tue, 16 Jun 2020 09:53:23: 8000000 INFO @ Tue, 16 Jun 2020 09:53:27: 15000000 INFO @ Tue, 16 Jun 2020 09:53:28: 9000000 INFO @ Tue, 16 Jun 2020 09:53:29: 3000000 INFO @ Tue, 16 Jun 2020 09:53:33: 16000000 INFO @ Tue, 16 Jun 2020 09:53:34: 10000000 INFO @ Tue, 16 Jun 2020 09:53:35: 4000000 INFO @ Tue, 16 Jun 2020 09:53:39: 17000000 INFO @ Tue, 16 Jun 2020 09:53:40: 11000000 INFO @ Tue, 16 Jun 2020 09:53:41: 5000000 INFO @ Tue, 16 Jun 2020 09:53:45: 18000000 INFO @ Tue, 16 Jun 2020 09:53:46: 12000000 INFO @ Tue, 16 Jun 2020 09:53:48: 6000000 INFO @ Tue, 16 Jun 2020 09:53:51: 19000000 INFO @ Tue, 16 Jun 2020 09:53:52: 13000000 INFO @ Tue, 16 Jun 2020 09:53:54: 7000000 INFO @ Tue, 16 Jun 2020 09:53:57: 20000000 INFO @ Tue, 16 Jun 2020 09:53:58: 14000000 INFO @ Tue, 16 Jun 2020 09:54:00: 8000000 INFO @ Tue, 16 Jun 2020 09:54:03: 21000000 INFO @ Tue, 16 Jun 2020 09:54:03: 15000000 INFO @ Tue, 16 Jun 2020 09:54:07: 9000000 INFO @ Tue, 16 Jun 2020 09:54:08: 22000000 INFO @ Tue, 16 Jun 2020 09:54:09: 16000000 INFO @ Tue, 16 Jun 2020 09:54:13: 10000000 INFO @ Tue, 16 Jun 2020 09:54:14: 23000000 INFO @ Tue, 16 Jun 2020 09:54:15: 17000000 INFO @ Tue, 16 Jun 2020 09:54:19: 11000000 INFO @ Tue, 16 Jun 2020 09:54:20: 24000000 INFO @ Tue, 16 Jun 2020 09:54:21: 18000000 INFO @ Tue, 16 Jun 2020 09:54:25: 12000000 INFO @ Tue, 16 Jun 2020 09:54:26: 25000000 INFO @ Tue, 16 Jun 2020 09:54:27: 19000000 INFO @ Tue, 16 Jun 2020 09:54:32: 13000000 INFO @ Tue, 16 Jun 2020 09:54:32: 26000000 INFO @ Tue, 16 Jun 2020 09:54:33: 20000000 INFO @ Tue, 16 Jun 2020 09:54:38: 27000000 INFO @ Tue, 16 Jun 2020 09:54:38: 14000000 INFO @ Tue, 16 Jun 2020 09:54:39: 21000000 INFO @ Tue, 16 Jun 2020 09:54:44: 28000000 INFO @ Tue, 16 Jun 2020 09:54:44: 15000000 INFO @ Tue, 16 Jun 2020 09:54:45: 22000000 INFO @ Tue, 16 Jun 2020 09:54:50: 29000000 INFO @ Tue, 16 Jun 2020 09:54:51: 16000000 INFO @ Tue, 16 Jun 2020 09:54:51: 23000000 INFO @ Tue, 16 Jun 2020 09:54:56: 30000000 INFO @ Tue, 16 Jun 2020 09:54:57: 24000000 INFO @ Tue, 16 Jun 2020 09:54:57: 17000000 INFO @ Tue, 16 Jun 2020 09:55:02: 31000000 INFO @ Tue, 16 Jun 2020 09:55:03: 25000000 INFO @ Tue, 16 Jun 2020 09:55:03: 18000000 INFO @ Tue, 16 Jun 2020 09:55:07: 32000000 INFO @ Tue, 16 Jun 2020 09:55:08: 26000000 INFO @ Tue, 16 Jun 2020 09:55:09: 19000000 INFO @ Tue, 16 Jun 2020 09:55:13: 33000000 INFO @ Tue, 16 Jun 2020 09:55:14: 27000000 INFO @ Tue, 16 Jun 2020 09:55:16: 20000000 INFO @ Tue, 16 Jun 2020 09:55:19: 34000000 INFO @ Tue, 16 Jun 2020 09:55:20: 28000000 INFO @ Tue, 16 Jun 2020 09:55:22: 21000000 INFO @ Tue, 16 Jun 2020 09:55:25: 35000000 INFO @ Tue, 16 Jun 2020 09:55:26: 29000000 INFO @ Tue, 16 Jun 2020 09:55:28: 22000000 INFO @ Tue, 16 Jun 2020 09:55:31: 36000000 INFO @ Tue, 16 Jun 2020 09:55:32: 30000000 INFO @ Tue, 16 Jun 2020 09:55:35: 23000000 INFO @ Tue, 16 Jun 2020 09:55:37: 37000000 INFO @ Tue, 16 Jun 2020 09:55:38: 31000000 INFO @ Tue, 16 Jun 2020 09:55:42: 24000000 INFO @ Tue, 16 Jun 2020 09:55:42: 38000000 INFO @ Tue, 16 Jun 2020 09:55:43: 32000000 INFO @ Tue, 16 Jun 2020 09:55:48: 25000000 INFO @ Tue, 16 Jun 2020 09:55:48: 39000000 INFO @ Tue, 16 Jun 2020 09:55:49: 33000000 INFO @ Tue, 16 Jun 2020 09:55:54: 40000000 INFO @ Tue, 16 Jun 2020 09:55:55: 26000000 INFO @ Tue, 16 Jun 2020 09:55:55: 34000000 INFO @ Tue, 16 Jun 2020 09:56:00: 41000000 INFO @ Tue, 16 Jun 2020 09:56:01: 35000000 INFO @ Tue, 16 Jun 2020 09:56:01: 27000000 INFO @ Tue, 16 Jun 2020 09:56:03: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:56:03: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:56:03: #1 total tags in treatment: 18962855 INFO @ Tue, 16 Jun 2020 09:56:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:56:03: #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 09:56:03: #1 tags after filtering in treatment: 17185816 INFO @ Tue, 16 Jun 2020 09:56:03: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 16 Jun 2020 09:56:03: #1 finished! INFO @ Tue, 16 Jun 2020 09:56:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:56:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:56:04: #2 number of paired peaks: 310 WARNING @ Tue, 16 Jun 2020 09:56:04: Fewer paired peaks (310) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 310 pairs to build model! INFO @ Tue, 16 Jun 2020 09:56:04: start model_add_line... INFO @ Tue, 16 Jun 2020 09:56:04: start X-correlation... INFO @ Tue, 16 Jun 2020 09:56:04: end of X-cor INFO @ Tue, 16 Jun 2020 09:56:04: #2 finished! INFO @ Tue, 16 Jun 2020 09:56:04: #2 predicted fragment length is 143 bps INFO @ Tue, 16 Jun 2020 09:56:04: #2 alternative fragment length(s) may be 3,143,164,170 bps INFO @ Tue, 16 Jun 2020 09:56:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4996821/SRX4996821.05_model.r INFO @ Tue, 16 Jun 2020 09:56:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:56:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:56:07: 36000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:56:08: 28000000 INFO @ Tue, 16 Jun 2020 09:56:12: 37000000 INFO @ Tue, 16 Jun 2020 09:56:14: 29000000 INFO @ Tue, 16 Jun 2020 09:56:18: 38000000 INFO @ Tue, 16 Jun 2020 09:56:21: 30000000 INFO @ Tue, 16 Jun 2020 09:56:24: 39000000 INFO @ Tue, 16 Jun 2020 09:56:28: 31000000 INFO @ Tue, 16 Jun 2020 09:56:29: 40000000 INFO @ Tue, 16 Jun 2020 09:56:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:56:34: 32000000 INFO @ Tue, 16 Jun 2020 09:56:35: 41000000 INFO @ Tue, 16 Jun 2020 09:56:38: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:56:38: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:56:38: #1 total tags in treatment: 18962855 INFO @ Tue, 16 Jun 2020 09:56:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:56:38: #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 09:56:38: #1 tags after filtering in treatment: 17185816 INFO @ Tue, 16 Jun 2020 09:56:38: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 16 Jun 2020 09:56:38: #1 finished! INFO @ Tue, 16 Jun 2020 09:56:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:56:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:56:39: #2 number of paired peaks: 310 WARNING @ Tue, 16 Jun 2020 09:56:39: Fewer paired peaks (310) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 310 pairs to build model! INFO @ Tue, 16 Jun 2020 09:56:39: start model_add_line... INFO @ Tue, 16 Jun 2020 09:56:39: start X-correlation... INFO @ Tue, 16 Jun 2020 09:56:39: end of X-cor INFO @ Tue, 16 Jun 2020 09:56:39: #2 finished! INFO @ Tue, 16 Jun 2020 09:56:39: #2 predicted fragment length is 143 bps INFO @ Tue, 16 Jun 2020 09:56:39: #2 alternative fragment length(s) may be 3,143,164,170 bps INFO @ Tue, 16 Jun 2020 09:56:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4996821/SRX4996821.10_model.r INFO @ Tue, 16 Jun 2020 09:56:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:56:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:56:41: 33000000 INFO @ Tue, 16 Jun 2020 09:56:47: 34000000 INFO @ Tue, 16 Jun 2020 09:56:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4996821/SRX4996821.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:56:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4996821/SRX4996821.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:56:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4996821/SRX4996821.05_summits.bed INFO @ Tue, 16 Jun 2020 09:56:49: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (457 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:56:53: 35000000 INFO @ Tue, 16 Jun 2020 09:56:59: 36000000 INFO @ Tue, 16 Jun 2020 09:57:05: 37000000 INFO @ Tue, 16 Jun 2020 09:57:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:57:11: 38000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:57:17: 39000000 INFO @ Tue, 16 Jun 2020 09:57:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4996821/SRX4996821.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:57:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4996821/SRX4996821.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:57:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4996821/SRX4996821.10_summits.bed INFO @ Tue, 16 Jun 2020 09:57:23: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (348 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:57:24: 40000000 INFO @ Tue, 16 Jun 2020 09:57:30: 41000000 INFO @ Tue, 16 Jun 2020 09:57:32: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:57:32: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:57:32: #1 total tags in treatment: 18962855 INFO @ Tue, 16 Jun 2020 09:57:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:57:32: #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 09:57:33: #1 tags after filtering in treatment: 17185816 INFO @ Tue, 16 Jun 2020 09:57:33: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 16 Jun 2020 09:57:33: #1 finished! INFO @ Tue, 16 Jun 2020 09:57:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:57:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:57:34: #2 number of paired peaks: 310 WARNING @ Tue, 16 Jun 2020 09:57:34: Fewer paired peaks (310) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 310 pairs to build model! INFO @ Tue, 16 Jun 2020 09:57:34: start model_add_line... INFO @ Tue, 16 Jun 2020 09:57:34: start X-correlation... INFO @ Tue, 16 Jun 2020 09:57:34: end of X-cor INFO @ Tue, 16 Jun 2020 09:57:34: #2 finished! INFO @ Tue, 16 Jun 2020 09:57:34: #2 predicted fragment length is 143 bps INFO @ Tue, 16 Jun 2020 09:57:34: #2 alternative fragment length(s) may be 3,143,164,170 bps INFO @ Tue, 16 Jun 2020 09:57:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4996821/SRX4996821.20_model.r INFO @ Tue, 16 Jun 2020 09:57:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:57:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:58:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:58:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4996821/SRX4996821.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:58:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4996821/SRX4996821.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:58:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4996821/SRX4996821.20_summits.bed INFO @ Tue, 16 Jun 2020 09:58:19: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (215 records, 4 fields): 1 millis CompletedMACS2peakCalling