Job ID = 6367817 SRX = SRX4085385 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:52:48 prefetch.2.10.7: 1) Downloading 'SRR7167414'... 2020-06-15T23:52:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:58:46 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:58:46 prefetch.2.10.7: 1) 'SRR7167414' was downloaded successfully Read 23416339 spots for SRR7167414/SRR7167414.sra Written 23416339 spots for SRR7167414/SRR7167414.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: 00:15:21 23416339 reads; of these: 23416339 (100.00%) were paired; of these: 7188651 (30.70%) aligned concordantly 0 times 13751089 (58.72%) aligned concordantly exactly 1 time 2476599 (10.58%) aligned concordantly >1 times ---- 7188651 pairs aligned concordantly 0 times; of these: 456541 (6.35%) aligned discordantly 1 time ---- 6732110 pairs aligned 0 times concordantly or discordantly; of these: 13464220 mates make up the pairs; of these: 9839969 (73.08%) aligned 0 times 3091736 (22.96%) aligned exactly 1 time 532515 (3.96%) aligned >1 times 78.99% overall alignment rate Time searching: 00:15:21 Overall time: 00:15:21 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 16 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] 1323517 / 16500625 = 0.0802 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 09:25:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085385/SRX4085385.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085385/SRX4085385.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085385/SRX4085385.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085385/SRX4085385.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 09:25:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:25:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:25:44: 1000000 INFO @ Tue, 16 Jun 2020 09:25:50: 2000000 INFO @ Tue, 16 Jun 2020 09:25:55: 3000000 INFO @ Tue, 16 Jun 2020 09:26:01: 4000000 INFO @ Tue, 16 Jun 2020 09:26:06: 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 09:26:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085385/SRX4085385.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085385/SRX4085385.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085385/SRX4085385.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085385/SRX4085385.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 09:26:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:26:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:26:13: 6000000 INFO @ Tue, 16 Jun 2020 09:26:16: 1000000 INFO @ Tue, 16 Jun 2020 09:26:20: 7000000 INFO @ Tue, 16 Jun 2020 09:26:24: 2000000 INFO @ Tue, 16 Jun 2020 09:26:27: 8000000 INFO @ Tue, 16 Jun 2020 09:26:32: 3000000 INFO @ Tue, 16 Jun 2020 09:26:34: 9000000 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 09:26:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085385/SRX4085385.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085385/SRX4085385.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085385/SRX4085385.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085385/SRX4085385.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 09:26:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:26:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:26:40: 4000000 INFO @ Tue, 16 Jun 2020 09:26:41: 10000000 INFO @ Tue, 16 Jun 2020 09:26:46: 1000000 INFO @ Tue, 16 Jun 2020 09:26:48: 5000000 INFO @ Tue, 16 Jun 2020 09:26:48: 11000000 INFO @ Tue, 16 Jun 2020 09:26:53: 2000000 INFO @ Tue, 16 Jun 2020 09:26:56: 12000000 INFO @ Tue, 16 Jun 2020 09:26:56: 6000000 INFO @ Tue, 16 Jun 2020 09:27:00: 3000000 INFO @ Tue, 16 Jun 2020 09:27:03: 13000000 INFO @ Tue, 16 Jun 2020 09:27:04: 7000000 INFO @ Tue, 16 Jun 2020 09:27:08: 4000000 INFO @ Tue, 16 Jun 2020 09:27:10: 14000000 INFO @ Tue, 16 Jun 2020 09:27:12: 8000000 INFO @ Tue, 16 Jun 2020 09:27:15: 5000000 INFO @ Tue, 16 Jun 2020 09:27:18: 15000000 INFO @ Tue, 16 Jun 2020 09:27:20: 9000000 INFO @ Tue, 16 Jun 2020 09:27:22: 6000000 INFO @ Tue, 16 Jun 2020 09:27:25: 16000000 INFO @ Tue, 16 Jun 2020 09:27:28: 10000000 INFO @ Tue, 16 Jun 2020 09:27:30: 7000000 INFO @ Tue, 16 Jun 2020 09:27:32: 17000000 INFO @ Tue, 16 Jun 2020 09:27:36: 11000000 INFO @ Tue, 16 Jun 2020 09:27:37: 8000000 INFO @ Tue, 16 Jun 2020 09:27:40: 18000000 INFO @ Tue, 16 Jun 2020 09:27:44: 12000000 INFO @ Tue, 16 Jun 2020 09:27:45: 9000000 INFO @ Tue, 16 Jun 2020 09:27:47: 19000000 INFO @ Tue, 16 Jun 2020 09:27:52: 10000000 INFO @ Tue, 16 Jun 2020 09:27:52: 13000000 INFO @ Tue, 16 Jun 2020 09:27:55: 20000000 INFO @ Tue, 16 Jun 2020 09:27:59: 11000000 INFO @ Tue, 16 Jun 2020 09:28:01: 14000000 INFO @ Tue, 16 Jun 2020 09:28:02: 21000000 INFO @ Tue, 16 Jun 2020 09:28:07: 12000000 INFO @ Tue, 16 Jun 2020 09:28:09: 15000000 INFO @ Tue, 16 Jun 2020 09:28:10: 22000000 INFO @ Tue, 16 Jun 2020 09:28:14: 13000000 INFO @ Tue, 16 Jun 2020 09:28:17: 23000000 INFO @ Tue, 16 Jun 2020 09:28:17: 16000000 INFO @ Tue, 16 Jun 2020 09:28:22: 14000000 INFO @ Tue, 16 Jun 2020 09:28:24: 24000000 INFO @ Tue, 16 Jun 2020 09:28:25: 17000000 INFO @ Tue, 16 Jun 2020 09:28:29: 15000000 INFO @ Tue, 16 Jun 2020 09:28:32: 25000000 INFO @ Tue, 16 Jun 2020 09:28:33: 18000000 INFO @ Tue, 16 Jun 2020 09:28:36: 16000000 INFO @ Tue, 16 Jun 2020 09:28:39: 26000000 INFO @ Tue, 16 Jun 2020 09:28:41: 19000000 INFO @ Tue, 16 Jun 2020 09:28:44: 17000000 INFO @ Tue, 16 Jun 2020 09:28:46: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:28:49: 20000000 INFO @ Tue, 16 Jun 2020 09:28:51: 18000000 INFO @ Tue, 16 Jun 2020 09:28:54: 28000000 INFO @ Tue, 16 Jun 2020 09:28:57: 21000000 INFO @ Tue, 16 Jun 2020 09:28:58: 19000000 INFO @ Tue, 16 Jun 2020 09:29:01: 29000000 INFO @ Tue, 16 Jun 2020 09:29:05: 22000000 INFO @ Tue, 16 Jun 2020 09:29:06: 20000000 INFO @ Tue, 16 Jun 2020 09:29:08: 30000000 INFO @ Tue, 16 Jun 2020 09:29:13: 23000000 INFO @ Tue, 16 Jun 2020 09:29:14: 21000000 INFO @ Tue, 16 Jun 2020 09:29:16: 31000000 INFO @ Tue, 16 Jun 2020 09:29:21: 22000000 INFO @ Tue, 16 Jun 2020 09:29:21: 24000000 INFO @ Tue, 16 Jun 2020 09:29:23: 32000000 INFO @ Tue, 16 Jun 2020 09:29:28: 23000000 INFO @ Tue, 16 Jun 2020 09:29:29: 25000000 INFO @ Tue, 16 Jun 2020 09:29:30: 33000000 INFO @ Tue, 16 Jun 2020 09:29:35: 24000000 INFO @ Tue, 16 Jun 2020 09:29:37: 34000000 INFO @ Tue, 16 Jun 2020 09:29:38: 26000000 INFO @ Tue, 16 Jun 2020 09:29:39: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:29:39: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:29:39: #1 total tags in treatment: 14923216 INFO @ Tue, 16 Jun 2020 09:29:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:29:39: #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 09:29:40: #1 tags after filtering in treatment: 12646318 INFO @ Tue, 16 Jun 2020 09:29:40: #1 Redundant rate of treatment: 0.15 INFO @ Tue, 16 Jun 2020 09:29:40: #1 finished! INFO @ Tue, 16 Jun 2020 09:29:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:29:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:29:40: #2 number of paired peaks: 250 WARNING @ Tue, 16 Jun 2020 09:29:40: Fewer paired peaks (250) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 250 pairs to build model! INFO @ Tue, 16 Jun 2020 09:29:40: start model_add_line... INFO @ Tue, 16 Jun 2020 09:29:41: start X-correlation... INFO @ Tue, 16 Jun 2020 09:29:41: end of X-cor INFO @ Tue, 16 Jun 2020 09:29:41: #2 finished! INFO @ Tue, 16 Jun 2020 09:29:41: #2 predicted fragment length is 99 bps INFO @ Tue, 16 Jun 2020 09:29:41: #2 alternative fragment length(s) may be 3,71,78,99 bps INFO @ Tue, 16 Jun 2020 09:29:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085385/SRX4085385.05_model.r WARNING @ Tue, 16 Jun 2020 09:29:41: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:29:41: #2 You may need to consider one of the other alternative d(s): 3,71,78,99 WARNING @ Tue, 16 Jun 2020 09:29:41: #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 09:29:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:29:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:29:42: 25000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:29:45: 27000000 INFO @ Tue, 16 Jun 2020 09:29:50: 26000000 INFO @ Tue, 16 Jun 2020 09:29:53: 28000000 INFO @ Tue, 16 Jun 2020 09:29:57: 27000000 INFO @ Tue, 16 Jun 2020 09:30:01: 29000000 INFO @ Tue, 16 Jun 2020 09:30:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:30:04: 28000000 INFO @ Tue, 16 Jun 2020 09:30:09: 30000000 INFO @ Tue, 16 Jun 2020 09:30:11: 29000000 INFO @ Tue, 16 Jun 2020 09:30:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085385/SRX4085385.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:30:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085385/SRX4085385.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:30:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085385/SRX4085385.05_summits.bed INFO @ Tue, 16 Jun 2020 09:30:14: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1839 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:30:17: 31000000 INFO @ Tue, 16 Jun 2020 09:30:18: 30000000 INFO @ Tue, 16 Jun 2020 09:30:25: 32000000 INFO @ Tue, 16 Jun 2020 09:30:25: 31000000 INFO @ Tue, 16 Jun 2020 09:30:33: 32000000 INFO @ Tue, 16 Jun 2020 09:30:33: 33000000 INFO @ Tue, 16 Jun 2020 09:30:40: 33000000 INFO @ Tue, 16 Jun 2020 09:30:41: 34000000 INFO @ Tue, 16 Jun 2020 09:30:44: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:30:44: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:30:44: #1 total tags in treatment: 14923216 INFO @ Tue, 16 Jun 2020 09:30:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:30:44: #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 09:30:44: #1 tags after filtering in treatment: 12646318 INFO @ Tue, 16 Jun 2020 09:30:44: #1 Redundant rate of treatment: 0.15 INFO @ Tue, 16 Jun 2020 09:30:44: #1 finished! INFO @ Tue, 16 Jun 2020 09:30:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:30:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:30:45: #2 number of paired peaks: 250 WARNING @ Tue, 16 Jun 2020 09:30:45: Fewer paired peaks (250) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 250 pairs to build model! INFO @ Tue, 16 Jun 2020 09:30:45: start model_add_line... INFO @ Tue, 16 Jun 2020 09:30:45: start X-correlation... INFO @ Tue, 16 Jun 2020 09:30:45: end of X-cor INFO @ Tue, 16 Jun 2020 09:30:45: #2 finished! INFO @ Tue, 16 Jun 2020 09:30:45: #2 predicted fragment length is 99 bps INFO @ Tue, 16 Jun 2020 09:30:45: #2 alternative fragment length(s) may be 3,71,78,99 bps INFO @ Tue, 16 Jun 2020 09:30:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085385/SRX4085385.10_model.r WARNING @ Tue, 16 Jun 2020 09:30:45: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:30:45: #2 You may need to consider one of the other alternative d(s): 3,71,78,99 WARNING @ Tue, 16 Jun 2020 09:30:45: #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 09:30:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:30:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:30:46: 34000000 INFO @ Tue, 16 Jun 2020 09:30:49: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:30:49: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:30:49: #1 total tags in treatment: 14923216 INFO @ Tue, 16 Jun 2020 09:30:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:30:49: #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 09:30:49: #1 tags after filtering in treatment: 12646318 INFO @ Tue, 16 Jun 2020 09:30:49: #1 Redundant rate of treatment: 0.15 INFO @ Tue, 16 Jun 2020 09:30:49: #1 finished! INFO @ Tue, 16 Jun 2020 09:30:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:30:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:30:50: #2 number of paired peaks: 250 WARNING @ Tue, 16 Jun 2020 09:30:50: Fewer paired peaks (250) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 250 pairs to build model! INFO @ Tue, 16 Jun 2020 09:30:50: start model_add_line... INFO @ Tue, 16 Jun 2020 09:30:50: start X-correlation... INFO @ Tue, 16 Jun 2020 09:30:50: end of X-cor INFO @ Tue, 16 Jun 2020 09:30:50: #2 finished! INFO @ Tue, 16 Jun 2020 09:30:50: #2 predicted fragment length is 99 bps INFO @ Tue, 16 Jun 2020 09:30:50: #2 alternative fragment length(s) may be 3,71,78,99 bps INFO @ Tue, 16 Jun 2020 09:30:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085385/SRX4085385.20_model.r WARNING @ Tue, 16 Jun 2020 09:30:50: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:30:50: #2 You may need to consider one of the other alternative d(s): 3,71,78,99 WARNING @ Tue, 16 Jun 2020 09:30:50: #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 09:30:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:30:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:31:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:31:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:31:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085385/SRX4085385.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:31:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085385/SRX4085385.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:31:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085385/SRX4085385.10_summits.bed INFO @ Tue, 16 Jun 2020 09:31:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (989 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:31:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085385/SRX4085385.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:31:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085385/SRX4085385.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:31:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085385/SRX4085385.20_summits.bed INFO @ Tue, 16 Jun 2020 09:31:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (363 records, 4 fields): 2 millis CompletedMACS2peakCalling