Job ID = 6367833 SRX = SRX4085401 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:37:44 prefetch.2.10.7: 1) Downloading 'SRR7167430'... 2020-06-15T23:37:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:45:21 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:45:21 prefetch.2.10.7: 1) 'SRR7167430' was downloaded successfully Read 21354776 spots for SRR7167430/SRR7167430.sra Written 21354776 spots for SRR7167430/SRR7167430.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: 00:16:21 21354776 reads; of these: 21354776 (100.00%) were paired; of these: 1245979 (5.83%) aligned concordantly 0 times 18187635 (85.17%) aligned concordantly exactly 1 time 1921162 (9.00%) aligned concordantly >1 times ---- 1245979 pairs aligned concordantly 0 times; of these: 76274 (6.12%) aligned discordantly 1 time ---- 1169705 pairs aligned 0 times concordantly or discordantly; of these: 2339410 mates make up the pairs; of these: 1758590 (75.17%) aligned 0 times 474660 (20.29%) aligned exactly 1 time 106160 (4.54%) aligned >1 times 95.88% overall alignment rate Time searching: 00:16:21 Overall time: 00:16:21 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] 11304791 / 20165157 = 0.5606 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 09:12:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085401/SRX4085401.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085401/SRX4085401.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085401/SRX4085401.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085401/SRX4085401.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 09:12:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:12:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:12:54: 1000000 INFO @ Tue, 16 Jun 2020 09:13:01: 2000000 INFO @ Tue, 16 Jun 2020 09:13:07: 3000000 INFO @ Tue, 16 Jun 2020 09:13:14: 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 09:13:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085401/SRX4085401.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085401/SRX4085401.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085401/SRX4085401.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085401/SRX4085401.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 09:13:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:13:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:13:21: 5000000 INFO @ Tue, 16 Jun 2020 09:13:24: 1000000 INFO @ Tue, 16 Jun 2020 09:13:27: 6000000 INFO @ Tue, 16 Jun 2020 09:13:30: 2000000 INFO @ Tue, 16 Jun 2020 09:13:34: 7000000 INFO @ Tue, 16 Jun 2020 09:13:37: 3000000 INFO @ Tue, 16 Jun 2020 09:13:41: 8000000 INFO @ Tue, 16 Jun 2020 09:13:43: 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 09:13:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085401/SRX4085401.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085401/SRX4085401.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085401/SRX4085401.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085401/SRX4085401.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 09:13:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:13:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:13:48: 9000000 INFO @ Tue, 16 Jun 2020 09:13:50: 5000000 INFO @ Tue, 16 Jun 2020 09:13:53: 1000000 INFO @ Tue, 16 Jun 2020 09:13:54: 10000000 INFO @ Tue, 16 Jun 2020 09:13:56: 6000000 INFO @ Tue, 16 Jun 2020 09:14:00: 2000000 INFO @ Tue, 16 Jun 2020 09:14:01: 11000000 INFO @ Tue, 16 Jun 2020 09:14:03: 7000000 INFO @ Tue, 16 Jun 2020 09:14:06: 3000000 INFO @ Tue, 16 Jun 2020 09:14:08: 12000000 INFO @ Tue, 16 Jun 2020 09:14:09: 8000000 INFO @ Tue, 16 Jun 2020 09:14:12: 4000000 INFO @ Tue, 16 Jun 2020 09:14:15: 13000000 INFO @ Tue, 16 Jun 2020 09:14:16: 9000000 INFO @ Tue, 16 Jun 2020 09:14:18: 5000000 INFO @ Tue, 16 Jun 2020 09:14:22: 14000000 INFO @ Tue, 16 Jun 2020 09:14:23: 10000000 INFO @ Tue, 16 Jun 2020 09:14:24: 6000000 INFO @ Tue, 16 Jun 2020 09:14:28: 15000000 INFO @ Tue, 16 Jun 2020 09:14:29: 11000000 INFO @ Tue, 16 Jun 2020 09:14:30: 7000000 INFO @ Tue, 16 Jun 2020 09:14:35: 16000000 INFO @ Tue, 16 Jun 2020 09:14:36: 12000000 INFO @ Tue, 16 Jun 2020 09:14:36: 8000000 INFO @ Tue, 16 Jun 2020 09:14:42: 17000000 INFO @ Tue, 16 Jun 2020 09:14:42: 9000000 INFO @ Tue, 16 Jun 2020 09:14:42: 13000000 INFO @ Tue, 16 Jun 2020 09:14:48: 10000000 INFO @ Tue, 16 Jun 2020 09:14:49: 18000000 INFO @ Tue, 16 Jun 2020 09:14:49: 14000000 INFO @ Tue, 16 Jun 2020 09:14:51: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:14:51: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:14:51: #1 total tags in treatment: 8832555 INFO @ Tue, 16 Jun 2020 09:14:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:14:51: #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 09:14:51: #1 tags after filtering in treatment: 7190037 INFO @ Tue, 16 Jun 2020 09:14:51: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 16 Jun 2020 09:14:51: #1 finished! INFO @ Tue, 16 Jun 2020 09:14:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:14:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:14:52: #2 number of paired peaks: 673 WARNING @ Tue, 16 Jun 2020 09:14:52: Fewer paired peaks (673) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 673 pairs to build model! INFO @ Tue, 16 Jun 2020 09:14:52: start model_add_line... INFO @ Tue, 16 Jun 2020 09:14:52: start X-correlation... INFO @ Tue, 16 Jun 2020 09:14:52: end of X-cor INFO @ Tue, 16 Jun 2020 09:14:52: #2 finished! INFO @ Tue, 16 Jun 2020 09:14:52: #2 predicted fragment length is 118 bps INFO @ Tue, 16 Jun 2020 09:14:52: #2 alternative fragment length(s) may be 118 bps INFO @ Tue, 16 Jun 2020 09:14:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085401/SRX4085401.05_model.r INFO @ Tue, 16 Jun 2020 09:14:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:14:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:14:55: 11000000 INFO @ Tue, 16 Jun 2020 09:14:56: 15000000 INFO @ Tue, 16 Jun 2020 09:15:01: 12000000 INFO @ Tue, 16 Jun 2020 09:15:02: 16000000 INFO @ Tue, 16 Jun 2020 09:15:07: 13000000 INFO @ Tue, 16 Jun 2020 09:15:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:15:09: 17000000 INFO @ Tue, 16 Jun 2020 09:15:13: 14000000 INFO @ Tue, 16 Jun 2020 09:15:15: 18000000 INFO @ Tue, 16 Jun 2020 09:15:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085401/SRX4085401.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:15:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085401/SRX4085401.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:15:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085401/SRX4085401.05_summits.bed INFO @ Tue, 16 Jun 2020 09:15:16: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (3518 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:15:17: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:15:17: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:15:17: #1 total tags in treatment: 8832555 INFO @ Tue, 16 Jun 2020 09:15:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:15:17: #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 09:15:17: #1 tags after filtering in treatment: 7190037 INFO @ Tue, 16 Jun 2020 09:15:17: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 16 Jun 2020 09:15:17: #1 finished! INFO @ Tue, 16 Jun 2020 09:15:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:15:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:15:18: #2 number of paired peaks: 673 WARNING @ Tue, 16 Jun 2020 09:15:18: Fewer paired peaks (673) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 673 pairs to build model! INFO @ Tue, 16 Jun 2020 09:15:18: start model_add_line... INFO @ Tue, 16 Jun 2020 09:15:18: start X-correlation... INFO @ Tue, 16 Jun 2020 09:15:18: end of X-cor INFO @ Tue, 16 Jun 2020 09:15:18: #2 finished! INFO @ Tue, 16 Jun 2020 09:15:18: #2 predicted fragment length is 118 bps INFO @ Tue, 16 Jun 2020 09:15:18: #2 alternative fragment length(s) may be 118 bps INFO @ Tue, 16 Jun 2020 09:15:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085401/SRX4085401.10_model.r INFO @ Tue, 16 Jun 2020 09:15:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:15:18: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:15:19: 15000000 INFO @ Tue, 16 Jun 2020 09:15:25: 16000000 INFO @ Tue, 16 Jun 2020 09:15:31: 17000000 INFO @ Tue, 16 Jun 2020 09:15:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:15:36: 18000000 INFO @ Tue, 16 Jun 2020 09:15:38: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:15:38: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:15:38: #1 total tags in treatment: 8832555 INFO @ Tue, 16 Jun 2020 09:15:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:15:38: #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 09:15:38: #1 tags after filtering in treatment: 7190037 INFO @ Tue, 16 Jun 2020 09:15:38: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 16 Jun 2020 09:15:38: #1 finished! INFO @ Tue, 16 Jun 2020 09:15:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:15:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:15:39: #2 number of paired peaks: 673 WARNING @ Tue, 16 Jun 2020 09:15:39: Fewer paired peaks (673) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 673 pairs to build model! INFO @ Tue, 16 Jun 2020 09:15:39: start model_add_line... INFO @ Tue, 16 Jun 2020 09:15:39: start X-correlation... INFO @ Tue, 16 Jun 2020 09:15:39: end of X-cor INFO @ Tue, 16 Jun 2020 09:15:39: #2 finished! INFO @ Tue, 16 Jun 2020 09:15:39: #2 predicted fragment length is 118 bps INFO @ Tue, 16 Jun 2020 09:15:39: #2 alternative fragment length(s) may be 118 bps INFO @ Tue, 16 Jun 2020 09:15:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085401/SRX4085401.20_model.r INFO @ Tue, 16 Jun 2020 09:15:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:15:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:15:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085401/SRX4085401.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:15:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085401/SRX4085401.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:15:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085401/SRX4085401.10_summits.bed INFO @ Tue, 16 Jun 2020 09:15:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2097 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:15:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:16:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085401/SRX4085401.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:16:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085401/SRX4085401.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:16:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085401/SRX4085401.20_summits.bed INFO @ Tue, 16 Jun 2020 09:16:03: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1101 records, 4 fields): 4 millis CompletedMACS2peakCalling