Job ID = 6368624 SRX = SRX5064640 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-16T00:21:36 prefetch.2.10.7: 1) Downloading 'SRR8246576'... 2020-06-16T00:21:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:33:19 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:33:19 prefetch.2.10.7: 1) 'SRR8246576' was downloaded successfully 2020-06-16T00:33:19 prefetch.2.10.7: 'SRR8246576' has 0 unresolved dependencies Read 27259598 spots for SRR8246576/SRR8246576.sra Written 27259598 spots for SRR8246576/SRR8246576.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: 01:30:23 27259598 reads; of these: 27259598 (100.00%) were paired; of these: 1876712 (6.88%) aligned concordantly 0 times 19208060 (70.46%) aligned concordantly exactly 1 time 6174826 (22.65%) aligned concordantly >1 times ---- 1876712 pairs aligned concordantly 0 times; of these: 374704 (19.97%) aligned discordantly 1 time ---- 1502008 pairs aligned 0 times concordantly or discordantly; of these: 3004016 mates make up the pairs; of these: 2350319 (78.24%) aligned 0 times 297829 (9.91%) aligned exactly 1 time 355868 (11.85%) aligned >1 times 95.69% overall alignment rate Time searching: 01:30:23 Overall time: 01:30:23 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 40 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] 7975704 / 25714987 = 0.3102 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 11:31:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5064640/SRX5064640.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5064640/SRX5064640.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5064640/SRX5064640.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5064640/SRX5064640.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 11:31:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 11:31:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 11:31:48: 1000000 INFO @ Tue, 16 Jun 2020 11:31:59: 2000000 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 11:32:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5064640/SRX5064640.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5064640/SRX5064640.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5064640/SRX5064640.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5064640/SRX5064640.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 11:32:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 11:32:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 11:32:09: 3000000 INFO @ Tue, 16 Jun 2020 11:32:19: 1000000 INFO @ Tue, 16 Jun 2020 11:32:20: 4000000 INFO @ Tue, 16 Jun 2020 11:32:29: 2000000 INFO @ Tue, 16 Jun 2020 11:32:30: 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 11:32:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5064640/SRX5064640.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5064640/SRX5064640.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5064640/SRX5064640.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5064640/SRX5064640.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 11:32:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 11:32:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 11:32:40: 6000000 INFO @ Tue, 16 Jun 2020 11:32:40: 3000000 INFO @ Tue, 16 Jun 2020 11:32:50: 7000000 INFO @ Tue, 16 Jun 2020 11:32:51: 1000000 INFO @ Tue, 16 Jun 2020 11:32:53: 4000000 INFO @ Tue, 16 Jun 2020 11:33:00: 8000000 INFO @ Tue, 16 Jun 2020 11:33:03: 2000000 INFO @ Tue, 16 Jun 2020 11:33:05: 5000000 INFO @ Tue, 16 Jun 2020 11:33:10: 9000000 INFO @ Tue, 16 Jun 2020 11:33:16: 3000000 INFO @ Tue, 16 Jun 2020 11:33:17: 6000000 INFO @ Tue, 16 Jun 2020 11:33:20: 10000000 INFO @ Tue, 16 Jun 2020 11:33:28: 4000000 INFO @ Tue, 16 Jun 2020 11:33:29: 7000000 INFO @ Tue, 16 Jun 2020 11:33:30: 11000000 INFO @ Tue, 16 Jun 2020 11:33:41: 5000000 INFO @ Tue, 16 Jun 2020 11:33:41: 12000000 INFO @ Tue, 16 Jun 2020 11:33:41: 8000000 INFO @ Tue, 16 Jun 2020 11:33:51: 13000000 INFO @ Tue, 16 Jun 2020 11:33:52: 6000000 INFO @ Tue, 16 Jun 2020 11:33:53: 9000000 INFO @ Tue, 16 Jun 2020 11:34:01: 14000000 INFO @ Tue, 16 Jun 2020 11:34:04: 7000000 INFO @ Tue, 16 Jun 2020 11:34:06: 10000000 INFO @ Tue, 16 Jun 2020 11:34:11: 15000000 INFO @ Tue, 16 Jun 2020 11:34:16: 8000000 INFO @ Tue, 16 Jun 2020 11:34:18: 11000000 INFO @ Tue, 16 Jun 2020 11:34:21: 16000000 INFO @ Tue, 16 Jun 2020 11:34:29: 9000000 INFO @ Tue, 16 Jun 2020 11:34:30: 12000000 INFO @ Tue, 16 Jun 2020 11:34:31: 17000000 INFO @ Tue, 16 Jun 2020 11:34:41: 10000000 INFO @ Tue, 16 Jun 2020 11:34:42: 13000000 INFO @ Tue, 16 Jun 2020 11:34:43: 18000000 INFO @ Tue, 16 Jun 2020 11:34:53: 11000000 INFO @ Tue, 16 Jun 2020 11:34:54: 14000000 INFO @ Tue, 16 Jun 2020 11:34:55: 19000000 INFO @ Tue, 16 Jun 2020 11:35:04: 12000000 INFO @ Tue, 16 Jun 2020 11:35:05: 15000000 INFO @ Tue, 16 Jun 2020 11:35:08: 20000000 INFO @ Tue, 16 Jun 2020 11:35:16: 13000000 INFO @ Tue, 16 Jun 2020 11:35:17: 16000000 INFO @ Tue, 16 Jun 2020 11:35:22: 21000000 INFO @ Tue, 16 Jun 2020 11:35:28: 14000000 INFO @ Tue, 16 Jun 2020 11:35:29: 17000000 INFO @ Tue, 16 Jun 2020 11:35:36: 22000000 INFO @ Tue, 16 Jun 2020 11:35:41: 15000000 INFO @ Tue, 16 Jun 2020 11:35:43: 18000000 INFO @ Tue, 16 Jun 2020 11:35:50: 23000000 INFO @ Tue, 16 Jun 2020 11:35:54: 16000000 INFO @ Tue, 16 Jun 2020 11:35:55: 19000000 INFO @ Tue, 16 Jun 2020 11:36:03: 24000000 INFO @ Tue, 16 Jun 2020 11:36:06: 17000000 INFO @ Tue, 16 Jun 2020 11:36:08: 20000000 INFO @ Tue, 16 Jun 2020 11:36:16: 25000000 INFO @ Tue, 16 Jun 2020 11:36:18: 18000000 INFO @ Tue, 16 Jun 2020 11:36:21: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 11:36:30: 26000000 INFO @ Tue, 16 Jun 2020 11:36:31: 19000000 INFO @ Tue, 16 Jun 2020 11:36:34: 22000000 INFO @ Tue, 16 Jun 2020 11:36:44: 20000000 INFO @ Tue, 16 Jun 2020 11:36:46: 27000000 INFO @ Tue, 16 Jun 2020 11:36:48: 23000000 INFO @ Tue, 16 Jun 2020 11:36:57: 21000000 INFO @ Tue, 16 Jun 2020 11:37:00: 28000000 INFO @ Tue, 16 Jun 2020 11:37:03: 24000000 INFO @ Tue, 16 Jun 2020 11:37:11: 22000000 INFO @ Tue, 16 Jun 2020 11:37:14: 29000000 INFO @ Tue, 16 Jun 2020 11:37:17: 25000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 11:37:25: 23000000 INFO @ Tue, 16 Jun 2020 11:37:29: 30000000 INFO @ Tue, 16 Jun 2020 11:37:31: 26000000 INFO @ Tue, 16 Jun 2020 11:37:40: 24000000 INFO @ Tue, 16 Jun 2020 11:37:47: 31000000 INFO @ Tue, 16 Jun 2020 11:37:47: 27000000 INFO @ Tue, 16 Jun 2020 11:37:57: 25000000 INFO @ Tue, 16 Jun 2020 11:38:05: 28000000 INFO @ Tue, 16 Jun 2020 11:38:12: 32000000 INFO @ Tue, 16 Jun 2020 11:38:13: 26000000 INFO @ Tue, 16 Jun 2020 11:38:19: 29000000 INFO @ Tue, 16 Jun 2020 11:38:28: 27000000 INFO @ Tue, 16 Jun 2020 11:38:28: 33000000 INFO @ Tue, 16 Jun 2020 11:38:35: 30000000 INFO @ Tue, 16 Jun 2020 11:38:44: 28000000 INFO @ Tue, 16 Jun 2020 11:38:45: 34000000 INFO @ Tue, 16 Jun 2020 11:38:50: 31000000 INFO @ Tue, 16 Jun 2020 11:38:59: 29000000 INFO @ Tue, 16 Jun 2020 11:38:59: 35000000 INFO @ Tue, 16 Jun 2020 11:39:06: 32000000 INFO @ Tue, 16 Jun 2020 11:39:13: 36000000 INFO @ Tue, 16 Jun 2020 11:39:13: 30000000 INFO @ Tue, 16 Jun 2020 11:39:16: #1 tag size is determined as 150 bps INFO @ Tue, 16 Jun 2020 11:39:16: #1 tag size = 150 INFO @ Tue, 16 Jun 2020 11:39:16: #1 total tags in treatment: 17472362 INFO @ Tue, 16 Jun 2020 11:39:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 11:39:16: #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 11:39:16: #1 tags after filtering in treatment: 13420732 INFO @ Tue, 16 Jun 2020 11:39:16: #1 Redundant rate of treatment: 0.23 INFO @ Tue, 16 Jun 2020 11:39:16: #1 finished! INFO @ Tue, 16 Jun 2020 11:39:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 11:39:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 11:39:17: #2 number of paired peaks: 2251 INFO @ Tue, 16 Jun 2020 11:39:17: start model_add_line... INFO @ Tue, 16 Jun 2020 11:39:17: start X-correlation... INFO @ Tue, 16 Jun 2020 11:39:17: end of X-cor INFO @ Tue, 16 Jun 2020 11:39:17: #2 finished! INFO @ Tue, 16 Jun 2020 11:39:17: #2 predicted fragment length is 226 bps INFO @ Tue, 16 Jun 2020 11:39:17: #2 alternative fragment length(s) may be 1,223,226,235,242,261 bps INFO @ Tue, 16 Jun 2020 11:39:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5064640/SRX5064640.05_model.r WARNING @ Tue, 16 Jun 2020 11:39:17: #2 Since the d (226) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 11:39:17: #2 You may need to consider one of the other alternative d(s): 1,223,226,235,242,261 WARNING @ Tue, 16 Jun 2020 11:39:17: #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 11:39:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 11:39:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 11:39:20: 33000000 INFO @ Tue, 16 Jun 2020 11:39:26: 31000000 INFO @ Tue, 16 Jun 2020 11:39:33: 34000000 INFO @ Tue, 16 Jun 2020 11:39:39: 32000000 INFO @ Tue, 16 Jun 2020 11:39:46: 35000000 INFO @ Tue, 16 Jun 2020 11:39:53: 33000000 INFO @ Tue, 16 Jun 2020 11:39:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 11:39:59: 36000000 INFO @ Tue, 16 Jun 2020 11:40:02: #1 tag size is determined as 150 bps INFO @ Tue, 16 Jun 2020 11:40:02: #1 tag size = 150 INFO @ Tue, 16 Jun 2020 11:40:02: #1 total tags in treatment: 17472362 INFO @ Tue, 16 Jun 2020 11:40:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 11:40:02: #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 11:40:02: #1 tags after filtering in treatment: 13420732 INFO @ Tue, 16 Jun 2020 11:40:02: #1 Redundant rate of treatment: 0.23 INFO @ Tue, 16 Jun 2020 11:40:02: #1 finished! INFO @ Tue, 16 Jun 2020 11:40:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 11:40:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 11:40:03: #2 number of paired peaks: 2251 INFO @ Tue, 16 Jun 2020 11:40:03: start model_add_line... INFO @ Tue, 16 Jun 2020 11:40:03: start X-correlation... INFO @ Tue, 16 Jun 2020 11:40:03: end of X-cor INFO @ Tue, 16 Jun 2020 11:40:03: #2 finished! INFO @ Tue, 16 Jun 2020 11:40:03: #2 predicted fragment length is 226 bps INFO @ Tue, 16 Jun 2020 11:40:03: #2 alternative fragment length(s) may be 1,223,226,235,242,261 bps INFO @ Tue, 16 Jun 2020 11:40:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5064640/SRX5064640.10_model.r WARNING @ Tue, 16 Jun 2020 11:40:03: #2 Since the d (226) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 11:40:03: #2 You may need to consider one of the other alternative d(s): 1,223,226,235,242,261 WARNING @ Tue, 16 Jun 2020 11:40:03: #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 11:40:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 11:40:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 11:40:05: 34000000 INFO @ Tue, 16 Jun 2020 11:40:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5064640/SRX5064640.05_peaks.xls INFO @ Tue, 16 Jun 2020 11:40:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5064640/SRX5064640.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 11:40:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5064640/SRX5064640.05_summits.bed INFO @ Tue, 16 Jun 2020 11:40:10: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (824 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 11:40:17: 35000000 INFO @ Tue, 16 Jun 2020 11:40:27: 36000000 INFO @ Tue, 16 Jun 2020 11:40:29: #1 tag size is determined as 150 bps INFO @ Tue, 16 Jun 2020 11:40:29: #1 tag size = 150 INFO @ Tue, 16 Jun 2020 11:40:29: #1 total tags in treatment: 17472362 INFO @ Tue, 16 Jun 2020 11:40:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 11:40:29: #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 11:40:30: #1 tags after filtering in treatment: 13420732 INFO @ Tue, 16 Jun 2020 11:40:30: #1 Redundant rate of treatment: 0.23 INFO @ Tue, 16 Jun 2020 11:40:30: #1 finished! INFO @ Tue, 16 Jun 2020 11:40:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 11:40:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 11:40:31: #2 number of paired peaks: 2251 INFO @ Tue, 16 Jun 2020 11:40:31: start model_add_line... INFO @ Tue, 16 Jun 2020 11:40:31: start X-correlation... INFO @ Tue, 16 Jun 2020 11:40:31: end of X-cor INFO @ Tue, 16 Jun 2020 11:40:31: #2 finished! INFO @ Tue, 16 Jun 2020 11:40:31: #2 predicted fragment length is 226 bps INFO @ Tue, 16 Jun 2020 11:40:31: #2 alternative fragment length(s) may be 1,223,226,235,242,261 bps INFO @ Tue, 16 Jun 2020 11:40:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5064640/SRX5064640.20_model.r WARNING @ Tue, 16 Jun 2020 11:40:31: #2 Since the d (226) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 11:40:31: #2 You may need to consider one of the other alternative d(s): 1,223,226,235,242,261 WARNING @ Tue, 16 Jun 2020 11:40:31: #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 11:40:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 11:40:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 11:40:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 11:40:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5064640/SRX5064640.10_peaks.xls INFO @ Tue, 16 Jun 2020 11:40:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5064640/SRX5064640.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 11:40:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5064640/SRX5064640.10_summits.bed INFO @ Tue, 16 Jun 2020 11:40:56: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (486 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 11:41:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 11:41:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5064640/SRX5064640.20_peaks.xls INFO @ Tue, 16 Jun 2020 11:41:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5064640/SRX5064640.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 11:41:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5064640/SRX5064640.20_summits.bed INFO @ Tue, 16 Jun 2020 11:41:23: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (289 records, 4 fields): 3 millis CompletedMACS2peakCalling