Job ID = 6367852 SRX = SRX4085420 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:40:29 prefetch.2.10.7: 1) Downloading 'SRR7167449'... 2020-06-15T23:40:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:47:00 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:47:00 prefetch.2.10.7: 1) 'SRR7167449' was downloaded successfully Read 19662544 spots for SRR7167449/SRR7167449.sra Written 19662544 spots for SRR7167449/SRR7167449.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: 00:13:18 19662544 reads; of these: 19662544 (100.00%) were paired; of these: 8586646 (43.67%) aligned concordantly 0 times 9372870 (47.67%) aligned concordantly exactly 1 time 1703028 (8.66%) aligned concordantly >1 times ---- 8586646 pairs aligned concordantly 0 times; of these: 415177 (4.84%) aligned discordantly 1 time ---- 8171469 pairs aligned 0 times concordantly or discordantly; of these: 16342938 mates make up the pairs; of these: 12412972 (75.95%) aligned 0 times 3390673 (20.75%) aligned exactly 1 time 539293 (3.30%) aligned >1 times 68.43% overall alignment rate Time searching: 00:13:18 Overall time: 00:13:18 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] 855376 / 11347445 = 0.0754 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 09:10:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085420/SRX4085420.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085420/SRX4085420.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085420/SRX4085420.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085420/SRX4085420.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 09:10:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:25: 1000000 INFO @ Tue, 16 Jun 2020 09:10:31: 2000000 INFO @ Tue, 16 Jun 2020 09:10:38: 3000000 INFO @ Tue, 16 Jun 2020 09:10:44: 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 09:10:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085420/SRX4085420.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085420/SRX4085420.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085420/SRX4085420.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085420/SRX4085420.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 09:10:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:50: 5000000 INFO @ Tue, 16 Jun 2020 09:10:55: 1000000 INFO @ Tue, 16 Jun 2020 09:10:57: 6000000 INFO @ Tue, 16 Jun 2020 09:11:02: 2000000 INFO @ Tue, 16 Jun 2020 09:11:03: 7000000 INFO @ Tue, 16 Jun 2020 09:11:09: 3000000 INFO @ Tue, 16 Jun 2020 09:11:10: 8000000 INFO @ Tue, 16 Jun 2020 09:11:15: 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 09:11:17: 9000000 INFO @ Tue, 16 Jun 2020 09:11:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085420/SRX4085420.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085420/SRX4085420.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085420/SRX4085420.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085420/SRX4085420.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 09:11:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:11:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:11:22: 5000000 INFO @ Tue, 16 Jun 2020 09:11:24: 10000000 INFO @ Tue, 16 Jun 2020 09:11:25: 1000000 INFO @ Tue, 16 Jun 2020 09:11:29: 6000000 INFO @ Tue, 16 Jun 2020 09:11:31: 11000000 INFO @ Tue, 16 Jun 2020 09:11:32: 2000000 INFO @ Tue, 16 Jun 2020 09:11:35: 7000000 INFO @ Tue, 16 Jun 2020 09:11:37: 12000000 INFO @ Tue, 16 Jun 2020 09:11:39: 3000000 INFO @ Tue, 16 Jun 2020 09:11:42: 8000000 INFO @ Tue, 16 Jun 2020 09:11:44: 13000000 INFO @ Tue, 16 Jun 2020 09:11:46: 4000000 INFO @ Tue, 16 Jun 2020 09:11:49: 9000000 INFO @ Tue, 16 Jun 2020 09:11:51: 14000000 INFO @ Tue, 16 Jun 2020 09:11:53: 5000000 INFO @ Tue, 16 Jun 2020 09:11:56: 10000000 INFO @ Tue, 16 Jun 2020 09:11:58: 15000000 INFO @ Tue, 16 Jun 2020 09:12:00: 6000000 INFO @ Tue, 16 Jun 2020 09:12:02: 11000000 INFO @ Tue, 16 Jun 2020 09:12:05: 16000000 INFO @ Tue, 16 Jun 2020 09:12:07: 7000000 INFO @ Tue, 16 Jun 2020 09:12:09: 12000000 INFO @ Tue, 16 Jun 2020 09:12:12: 17000000 INFO @ Tue, 16 Jun 2020 09:12:14: 8000000 INFO @ Tue, 16 Jun 2020 09:12:16: 13000000 INFO @ Tue, 16 Jun 2020 09:12:19: 18000000 INFO @ Tue, 16 Jun 2020 09:12:22: 9000000 INFO @ Tue, 16 Jun 2020 09:12:23: 14000000 INFO @ Tue, 16 Jun 2020 09:12:26: 19000000 INFO @ Tue, 16 Jun 2020 09:12:29: 15000000 INFO @ Tue, 16 Jun 2020 09:12:29: 10000000 INFO @ Tue, 16 Jun 2020 09:12:33: 20000000 INFO @ Tue, 16 Jun 2020 09:12:36: 16000000 INFO @ Tue, 16 Jun 2020 09:12:37: 11000000 INFO @ Tue, 16 Jun 2020 09:12:39: 21000000 INFO @ Tue, 16 Jun 2020 09:12:43: 17000000 INFO @ Tue, 16 Jun 2020 09:12:44: 12000000 INFO @ Tue, 16 Jun 2020 09:12:46: 22000000 INFO @ Tue, 16 Jun 2020 09:12:50: 18000000 INFO @ Tue, 16 Jun 2020 09:12:51: 13000000 INFO @ Tue, 16 Jun 2020 09:12:53: 23000000 INFO @ Tue, 16 Jun 2020 09:12:56: 19000000 INFO @ Tue, 16 Jun 2020 09:12:58: 14000000 INFO @ Tue, 16 Jun 2020 09:13:00: 24000000 INFO @ Tue, 16 Jun 2020 09:13:03: 20000000 INFO @ Tue, 16 Jun 2020 09:13:05: 15000000 INFO @ Tue, 16 Jun 2020 09:13:07: 25000000 INFO @ Tue, 16 Jun 2020 09:13:08: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:13:08: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:13:08: #1 total tags in treatment: 10243257 INFO @ Tue, 16 Jun 2020 09:13:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:13:08: #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 09:13:08: #1 tags after filtering in treatment: 9140481 INFO @ Tue, 16 Jun 2020 09:13:08: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 16 Jun 2020 09:13:08: #1 finished! INFO @ Tue, 16 Jun 2020 09:13:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:13:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:13:09: #2 number of paired peaks: 360 WARNING @ Tue, 16 Jun 2020 09:13:09: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Tue, 16 Jun 2020 09:13:09: start model_add_line... INFO @ Tue, 16 Jun 2020 09:13:09: start X-correlation... INFO @ Tue, 16 Jun 2020 09:13:09: end of X-cor INFO @ Tue, 16 Jun 2020 09:13:09: #2 finished! INFO @ Tue, 16 Jun 2020 09:13:09: #2 predicted fragment length is 112 bps INFO @ Tue, 16 Jun 2020 09:13:09: #2 alternative fragment length(s) may be 112,588,597 bps INFO @ Tue, 16 Jun 2020 09:13:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085420/SRX4085420.05_model.r INFO @ Tue, 16 Jun 2020 09:13:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:13:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:13:10: 21000000 INFO @ Tue, 16 Jun 2020 09:13:12: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:13:17: 22000000 INFO @ Tue, 16 Jun 2020 09:13:19: 17000000 INFO @ Tue, 16 Jun 2020 09:13:24: 23000000 INFO @ Tue, 16 Jun 2020 09:13:25: 18000000 INFO @ Tue, 16 Jun 2020 09:13:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:13:30: 24000000 INFO @ Tue, 16 Jun 2020 09:13:32: 19000000 INFO @ Tue, 16 Jun 2020 09:13:37: 25000000 INFO @ Tue, 16 Jun 2020 09:13:38: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:13:38: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:13:38: #1 total tags in treatment: 10243257 INFO @ Tue, 16 Jun 2020 09:13:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:13:38: #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 09:13:39: #1 tags after filtering in treatment: 9140481 INFO @ Tue, 16 Jun 2020 09:13:39: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 16 Jun 2020 09:13:39: #1 finished! INFO @ Tue, 16 Jun 2020 09:13:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:13:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:13:39: 20000000 INFO @ Tue, 16 Jun 2020 09:13:39: #2 number of paired peaks: 360 WARNING @ Tue, 16 Jun 2020 09:13:39: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Tue, 16 Jun 2020 09:13:39: start model_add_line... INFO @ Tue, 16 Jun 2020 09:13:39: start X-correlation... INFO @ Tue, 16 Jun 2020 09:13:39: end of X-cor INFO @ Tue, 16 Jun 2020 09:13:39: #2 finished! INFO @ Tue, 16 Jun 2020 09:13:39: #2 predicted fragment length is 112 bps INFO @ Tue, 16 Jun 2020 09:13:39: #2 alternative fragment length(s) may be 112,588,597 bps INFO @ Tue, 16 Jun 2020 09:13:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085420/SRX4085420.10_model.r INFO @ Tue, 16 Jun 2020 09:13:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:13:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:13:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085420/SRX4085420.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:13:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085420/SRX4085420.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:13:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085420/SRX4085420.05_summits.bed INFO @ Tue, 16 Jun 2020 09:13:40: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2480 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:13:45: 21000000 INFO @ Tue, 16 Jun 2020 09:13:52: 22000000 INFO @ Tue, 16 Jun 2020 09:13:58: 23000000 INFO @ Tue, 16 Jun 2020 09:14:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:14:04: 24000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:14:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085420/SRX4085420.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:14:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085420/SRX4085420.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:14:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085420/SRX4085420.10_summits.bed INFO @ Tue, 16 Jun 2020 09:14:10: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1427 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:14:10: 25000000 INFO @ Tue, 16 Jun 2020 09:14:12: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:14:12: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:14:12: #1 total tags in treatment: 10243257 INFO @ Tue, 16 Jun 2020 09:14:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:14:12: #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 09:14:12: #1 tags after filtering in treatment: 9140481 INFO @ Tue, 16 Jun 2020 09:14:12: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 16 Jun 2020 09:14:12: #1 finished! INFO @ Tue, 16 Jun 2020 09:14:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:14:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:14:13: #2 number of paired peaks: 360 WARNING @ Tue, 16 Jun 2020 09:14:13: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Tue, 16 Jun 2020 09:14:13: start model_add_line... INFO @ Tue, 16 Jun 2020 09:14:13: start X-correlation... INFO @ Tue, 16 Jun 2020 09:14:13: end of X-cor INFO @ Tue, 16 Jun 2020 09:14:13: #2 finished! INFO @ Tue, 16 Jun 2020 09:14:13: #2 predicted fragment length is 112 bps INFO @ Tue, 16 Jun 2020 09:14:13: #2 alternative fragment length(s) may be 112,588,597 bps INFO @ Tue, 16 Jun 2020 09:14:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085420/SRX4085420.20_model.r INFO @ Tue, 16 Jun 2020 09:14:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:14:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:14:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:14:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085420/SRX4085420.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:14:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085420/SRX4085420.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:14:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085420/SRX4085420.20_summits.bed INFO @ Tue, 16 Jun 2020 09:14:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (670 records, 4 fields): 2 millis CompletedMACS2peakCalling