Job ID = 6368626 SRX = SRX5064642 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-16T00:20:51 prefetch.2.10.7: 1) Downloading 'SRR8246578'... 2020-06-16T00:20:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:27:21 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:27:21 prefetch.2.10.7: 1) 'SRR8246578' was downloaded successfully 2020-06-16T00:27:21 prefetch.2.10.7: 'SRR8246578' has 0 unresolved dependencies Read 16090837 spots for SRR8246578/SRR8246578.sra Written 16090837 spots for SRR8246578/SRR8246578.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: 00:32:58 16090837 reads; of these: 16090837 (100.00%) were paired; of these: 590705 (3.67%) aligned concordantly 0 times 14466076 (89.90%) aligned concordantly exactly 1 time 1034056 (6.43%) aligned concordantly >1 times ---- 590705 pairs aligned concordantly 0 times; of these: 234101 (39.63%) aligned discordantly 1 time ---- 356604 pairs aligned 0 times concordantly or discordantly; of these: 713208 mates make up the pairs; of these: 553514 (77.61%) aligned 0 times 112326 (15.75%) aligned exactly 1 time 47368 (6.64%) aligned >1 times 98.28% overall alignment rate Time searching: 00:32:58 Overall time: 00:32:58 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 24 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] 4486103 / 15716570 = 0.2854 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 10:17:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5064642/SRX5064642.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5064642/SRX5064642.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5064642/SRX5064642.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5064642/SRX5064642.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 10:17:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:17:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:17:35: 1000000 INFO @ Tue, 16 Jun 2020 10:17:43: 2000000 INFO @ Tue, 16 Jun 2020 10:17:52: 3000000 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 10:17:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5064642/SRX5064642.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5064642/SRX5064642.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5064642/SRX5064642.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5064642/SRX5064642.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 10:17:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:17:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:18:00: 4000000 INFO @ Tue, 16 Jun 2020 10:18:04: 1000000 INFO @ Tue, 16 Jun 2020 10:18:09: 5000000 INFO @ Tue, 16 Jun 2020 10:18:12: 2000000 INFO @ Tue, 16 Jun 2020 10:18:18: 6000000 INFO @ Tue, 16 Jun 2020 10:18:20: 3000000 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 10:18:26: 7000000 INFO @ Tue, 16 Jun 2020 10:18:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5064642/SRX5064642.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5064642/SRX5064642.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5064642/SRX5064642.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5064642/SRX5064642.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 10:18:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:18:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:18:28: 4000000 INFO @ Tue, 16 Jun 2020 10:18:34: 8000000 INFO @ Tue, 16 Jun 2020 10:18:36: 1000000 INFO @ Tue, 16 Jun 2020 10:18:37: 5000000 INFO @ Tue, 16 Jun 2020 10:18:42: 9000000 INFO @ Tue, 16 Jun 2020 10:18:45: 2000000 INFO @ Tue, 16 Jun 2020 10:18:46: 6000000 INFO @ Tue, 16 Jun 2020 10:18:50: 10000000 INFO @ Tue, 16 Jun 2020 10:18:54: 3000000 INFO @ Tue, 16 Jun 2020 10:18:55: 7000000 INFO @ Tue, 16 Jun 2020 10:18:58: 11000000 INFO @ Tue, 16 Jun 2020 10:19:03: 4000000 INFO @ Tue, 16 Jun 2020 10:19:04: 8000000 INFO @ Tue, 16 Jun 2020 10:19:06: 12000000 INFO @ Tue, 16 Jun 2020 10:19:12: 5000000 INFO @ Tue, 16 Jun 2020 10:19:13: 9000000 INFO @ Tue, 16 Jun 2020 10:19:15: 13000000 INFO @ Tue, 16 Jun 2020 10:19:21: 6000000 INFO @ Tue, 16 Jun 2020 10:19:22: 10000000 INFO @ Tue, 16 Jun 2020 10:19:23: 14000000 INFO @ Tue, 16 Jun 2020 10:19:31: 7000000 INFO @ Tue, 16 Jun 2020 10:19:31: 15000000 INFO @ Tue, 16 Jun 2020 10:19:31: 11000000 INFO @ Tue, 16 Jun 2020 10:19:39: 16000000 INFO @ Tue, 16 Jun 2020 10:19:40: 8000000 INFO @ Tue, 16 Jun 2020 10:19:40: 12000000 INFO @ Tue, 16 Jun 2020 10:19:47: 17000000 INFO @ Tue, 16 Jun 2020 10:19:48: 9000000 INFO @ Tue, 16 Jun 2020 10:19:49: 13000000 INFO @ Tue, 16 Jun 2020 10:19:55: 18000000 INFO @ Tue, 16 Jun 2020 10:19:57: 14000000 INFO @ Tue, 16 Jun 2020 10:19:58: 10000000 INFO @ Tue, 16 Jun 2020 10:20:03: 19000000 INFO @ Tue, 16 Jun 2020 10:20:05: 15000000 INFO @ Tue, 16 Jun 2020 10:20:07: 11000000 INFO @ Tue, 16 Jun 2020 10:20:11: 20000000 INFO @ Tue, 16 Jun 2020 10:20:14: 16000000 INFO @ Tue, 16 Jun 2020 10:20:16: 12000000 INFO @ Tue, 16 Jun 2020 10:20:19: 21000000 INFO @ Tue, 16 Jun 2020 10:20:22: 17000000 INFO @ Tue, 16 Jun 2020 10:20:25: 13000000 INFO @ Tue, 16 Jun 2020 10:20:27: 22000000 INFO @ Tue, 16 Jun 2020 10:20:31: 18000000 INFO @ Tue, 16 Jun 2020 10:20:32: #1 tag size is determined as 150 bps INFO @ Tue, 16 Jun 2020 10:20:32: #1 tag size = 150 INFO @ Tue, 16 Jun 2020 10:20:32: #1 total tags in treatment: 11062859 INFO @ Tue, 16 Jun 2020 10:20:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:20:32: #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 10:20:33: #1 tags after filtering in treatment: 9630302 INFO @ Tue, 16 Jun 2020 10:20:33: #1 Redundant rate of treatment: 0.13 INFO @ Tue, 16 Jun 2020 10:20:33: #1 finished! INFO @ Tue, 16 Jun 2020 10:20:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:20:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:20:34: #2 number of paired peaks: 4084 INFO @ Tue, 16 Jun 2020 10:20:34: start model_add_line... INFO @ Tue, 16 Jun 2020 10:20:34: 14000000 INFO @ Tue, 16 Jun 2020 10:20:34: start X-correlation... INFO @ Tue, 16 Jun 2020 10:20:34: end of X-cor INFO @ Tue, 16 Jun 2020 10:20:34: #2 finished! INFO @ Tue, 16 Jun 2020 10:20:34: #2 predicted fragment length is 280 bps INFO @ Tue, 16 Jun 2020 10:20:34: #2 alternative fragment length(s) may be 280 bps INFO @ Tue, 16 Jun 2020 10:20:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5064642/SRX5064642.05_model.r WARNING @ Tue, 16 Jun 2020 10:20:34: #2 Since the d (280) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:20:34: #2 You may need to consider one of the other alternative d(s): 280 WARNING @ Tue, 16 Jun 2020 10:20:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 10:20:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:20:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:20:40: 19000000 INFO @ Tue, 16 Jun 2020 10:20:42: 15000000 INFO @ Tue, 16 Jun 2020 10:20:49: 20000000 INFO @ Tue, 16 Jun 2020 10:20:50: 16000000 INFO @ Tue, 16 Jun 2020 10:20:57: 21000000 INFO @ Tue, 16 Jun 2020 10:20:58: 17000000 INFO @ Tue, 16 Jun 2020 10:21:05: 22000000 INFO @ Tue, 16 Jun 2020 10:21:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:21:06: 18000000 INFO @ Tue, 16 Jun 2020 10:21:11: #1 tag size is determined as 150 bps INFO @ Tue, 16 Jun 2020 10:21:11: #1 tag size = 150 INFO @ Tue, 16 Jun 2020 10:21:11: #1 total tags in treatment: 11062859 INFO @ Tue, 16 Jun 2020 10:21:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:21:11: #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 10:21:11: #1 tags after filtering in treatment: 9630302 INFO @ Tue, 16 Jun 2020 10:21:11: #1 Redundant rate of treatment: 0.13 INFO @ Tue, 16 Jun 2020 10:21:11: #1 finished! INFO @ Tue, 16 Jun 2020 10:21:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:21:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:21:12: #2 number of paired peaks: 4084 INFO @ Tue, 16 Jun 2020 10:21:12: start model_add_line... INFO @ Tue, 16 Jun 2020 10:21:12: start X-correlation... INFO @ Tue, 16 Jun 2020 10:21:12: end of X-cor INFO @ Tue, 16 Jun 2020 10:21:12: #2 finished! INFO @ Tue, 16 Jun 2020 10:21:12: #2 predicted fragment length is 280 bps INFO @ Tue, 16 Jun 2020 10:21:12: #2 alternative fragment length(s) may be 280 bps INFO @ Tue, 16 Jun 2020 10:21:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5064642/SRX5064642.10_model.r WARNING @ Tue, 16 Jun 2020 10:21:12: #2 Since the d (280) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:21:12: #2 You may need to consider one of the other alternative d(s): 280 WARNING @ Tue, 16 Jun 2020 10:21:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 10:21:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:21:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:21:14: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:21:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5064642/SRX5064642.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:21:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5064642/SRX5064642.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:21:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5064642/SRX5064642.05_summits.bed INFO @ Tue, 16 Jun 2020 10:21:17: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (5634 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:21:21: 20000000 INFO @ Tue, 16 Jun 2020 10:21:28: 21000000 INFO @ Tue, 16 Jun 2020 10:21:35: 22000000 INFO @ Tue, 16 Jun 2020 10:21:40: #1 tag size is determined as 150 bps INFO @ Tue, 16 Jun 2020 10:21:40: #1 tag size = 150 INFO @ Tue, 16 Jun 2020 10:21:40: #1 total tags in treatment: 11062859 INFO @ Tue, 16 Jun 2020 10:21:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:21:40: #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 10:21:40: #1 tags after filtering in treatment: 9630302 INFO @ Tue, 16 Jun 2020 10:21:40: #1 Redundant rate of treatment: 0.13 INFO @ Tue, 16 Jun 2020 10:21:40: #1 finished! INFO @ Tue, 16 Jun 2020 10:21:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:21:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:21:41: #2 number of paired peaks: 4084 INFO @ Tue, 16 Jun 2020 10:21:41: start model_add_line... INFO @ Tue, 16 Jun 2020 10:21:41: start X-correlation... INFO @ Tue, 16 Jun 2020 10:21:41: end of X-cor INFO @ Tue, 16 Jun 2020 10:21:41: #2 finished! INFO @ Tue, 16 Jun 2020 10:21:41: #2 predicted fragment length is 280 bps INFO @ Tue, 16 Jun 2020 10:21:41: #2 alternative fragment length(s) may be 280 bps INFO @ Tue, 16 Jun 2020 10:21:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5064642/SRX5064642.20_model.r WARNING @ Tue, 16 Jun 2020 10:21:41: #2 Since the d (280) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:21:41: #2 You may need to consider one of the other alternative d(s): 280 WARNING @ Tue, 16 Jun 2020 10:21:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 10:21:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:21:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:21:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:21:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5064642/SRX5064642.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:21:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5064642/SRX5064642.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:21:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5064642/SRX5064642.10_summits.bed INFO @ Tue, 16 Jun 2020 10:21:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4421 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:22:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:22:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5064642/SRX5064642.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:22:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5064642/SRX5064642.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:22:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5064642/SRX5064642.20_summits.bed INFO @ Tue, 16 Jun 2020 10:22:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3292 records, 4 fields): 6 millis CompletedMACS2peakCalling