Job ID = 6507792 SRX = SRX4085369 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T15:23:37 prefetch.2.10.7: 1) Downloading 'SRR7167398'... 2020-06-26T15:23:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T15:27:39 prefetch.2.10.7: HTTPS download succeed 2020-06-26T15:27:39 prefetch.2.10.7: 1) 'SRR7167398' was downloaded successfully Read 20071556 spots for SRR7167398/SRR7167398.sra Written 20071556 spots for SRR7167398/SRR7167398.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:17:11 20071556 reads; of these: 20071556 (100.00%) were paired; of these: 6781814 (33.79%) aligned concordantly 0 times 11623309 (57.91%) aligned concordantly exactly 1 time 1666433 (8.30%) aligned concordantly >1 times ---- 6781814 pairs aligned concordantly 0 times; of these: 346952 (5.12%) aligned discordantly 1 time ---- 6434862 pairs aligned 0 times concordantly or discordantly; of these: 12869724 mates make up the pairs; of these: 9940897 (77.24%) aligned 0 times 2580770 (20.05%) aligned exactly 1 time 348057 (2.70%) aligned >1 times 75.24% overall alignment rate Time searching: 00:17:12 Overall time: 00:17:12 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] 1149900 / 13516619 = 0.0851 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 @ Sat, 27 Jun 2020 00:58:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085369/SRX4085369.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085369/SRX4085369.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085369/SRX4085369.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085369/SRX4085369.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 @ Sat, 27 Jun 2020 00:58:06: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:58:06: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:58:14: 1000000 INFO @ Sat, 27 Jun 2020 00:58:21: 2000000 INFO @ Sat, 27 Jun 2020 00:58:29: 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 @ Sat, 27 Jun 2020 00:58:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085369/SRX4085369.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085369/SRX4085369.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085369/SRX4085369.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085369/SRX4085369.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 @ Sat, 27 Jun 2020 00:58:35: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:58:35: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:58:37: 4000000 INFO @ Sat, 27 Jun 2020 00:58:44: 1000000 INFO @ Sat, 27 Jun 2020 00:58:45: 5000000 INFO @ Sat, 27 Jun 2020 00:58:51: 2000000 INFO @ Sat, 27 Jun 2020 00:58:54: 6000000 INFO @ Sat, 27 Jun 2020 00:58:59: 3000000 INFO @ Sat, 27 Jun 2020 00:59:02: 7000000 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 @ Sat, 27 Jun 2020 00:59:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085369/SRX4085369.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085369/SRX4085369.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085369/SRX4085369.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085369/SRX4085369.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 @ Sat, 27 Jun 2020 00:59:05: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:59:05: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:59:07: 4000000 INFO @ Sat, 27 Jun 2020 00:59:10: 8000000 INFO @ Sat, 27 Jun 2020 00:59:14: 1000000 INFO @ Sat, 27 Jun 2020 00:59:15: 5000000 INFO @ Sat, 27 Jun 2020 00:59:18: 9000000 INFO @ Sat, 27 Jun 2020 00:59:23: 2000000 INFO @ Sat, 27 Jun 2020 00:59:24: 6000000 INFO @ Sat, 27 Jun 2020 00:59:26: 10000000 INFO @ Sat, 27 Jun 2020 00:59:32: 7000000 INFO @ Sat, 27 Jun 2020 00:59:33: 3000000 INFO @ Sat, 27 Jun 2020 00:59:35: 11000000 INFO @ Sat, 27 Jun 2020 00:59:40: 8000000 INFO @ Sat, 27 Jun 2020 00:59:42: 4000000 INFO @ Sat, 27 Jun 2020 00:59:43: 12000000 INFO @ Sat, 27 Jun 2020 00:59:48: 9000000 INFO @ Sat, 27 Jun 2020 00:59:51: 5000000 INFO @ Sat, 27 Jun 2020 00:59:52: 13000000 INFO @ Sat, 27 Jun 2020 00:59:56: 10000000 INFO @ Sat, 27 Jun 2020 00:59:59: 6000000 INFO @ Sat, 27 Jun 2020 01:00:00: 14000000 INFO @ Sat, 27 Jun 2020 01:00:04: 11000000 INFO @ Sat, 27 Jun 2020 01:00:08: 7000000 INFO @ Sat, 27 Jun 2020 01:00:09: 15000000 INFO @ Sat, 27 Jun 2020 01:00:12: 12000000 INFO @ Sat, 27 Jun 2020 01:00:17: 16000000 INFO @ Sat, 27 Jun 2020 01:00:17: 8000000 INFO @ Sat, 27 Jun 2020 01:00:20: 13000000 INFO @ Sat, 27 Jun 2020 01:00:25: 17000000 INFO @ Sat, 27 Jun 2020 01:00:26: 9000000 INFO @ Sat, 27 Jun 2020 01:00:28: 14000000 INFO @ Sat, 27 Jun 2020 01:00:34: 18000000 INFO @ Sat, 27 Jun 2020 01:00:35: 10000000 INFO @ Sat, 27 Jun 2020 01:00:36: 15000000 INFO @ Sat, 27 Jun 2020 01:00:42: 19000000 INFO @ Sat, 27 Jun 2020 01:00:44: 11000000 INFO @ Sat, 27 Jun 2020 01:00:45: 16000000 INFO @ Sat, 27 Jun 2020 01:00:50: 20000000 INFO @ Sat, 27 Jun 2020 01:00:53: 17000000 INFO @ Sat, 27 Jun 2020 01:00:53: 12000000 INFO @ Sat, 27 Jun 2020 01:00:58: 21000000 INFO @ Sat, 27 Jun 2020 01:01:01: 18000000 INFO @ Sat, 27 Jun 2020 01:01:02: 13000000 INFO @ Sat, 27 Jun 2020 01:01:06: 22000000 INFO @ Sat, 27 Jun 2020 01:01:09: 19000000 INFO @ Sat, 27 Jun 2020 01:01:11: 14000000 INFO @ Sat, 27 Jun 2020 01:01:14: 23000000 INFO @ Sat, 27 Jun 2020 01:01:17: 20000000 INFO @ Sat, 27 Jun 2020 01:01:20: 15000000 INFO @ Sat, 27 Jun 2020 01:01:22: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 27 Jun 2020 01:01:25: 21000000 INFO @ Sat, 27 Jun 2020 01:01:28: 16000000 INFO @ Sat, 27 Jun 2020 01:01:31: 25000000 INFO @ Sat, 27 Jun 2020 01:01:33: 22000000 INFO @ Sat, 27 Jun 2020 01:01:37: 17000000 INFO @ Sat, 27 Jun 2020 01:01:39: 26000000 INFO @ Sat, 27 Jun 2020 01:01:41: 23000000 INFO @ Sat, 27 Jun 2020 01:01:46: 18000000 INFO @ Sat, 27 Jun 2020 01:01:47: 27000000 INFO @ Sat, 27 Jun 2020 01:01:49: 24000000 INFO @ Sat, 27 Jun 2020 01:01:54: #1 tag size is determined as 51 bps INFO @ Sat, 27 Jun 2020 01:01:54: #1 tag size = 51 INFO @ Sat, 27 Jun 2020 01:01:54: #1 total tags in treatment: 12159013 INFO @ Sat, 27 Jun 2020 01:01:54: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 01:01:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 01:01:54: #1 tags after filtering in treatment: 10404909 INFO @ Sat, 27 Jun 2020 01:01:54: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 27 Jun 2020 01:01:54: #1 finished! INFO @ Sat, 27 Jun 2020 01:01:54: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 01:01:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 01:01:54: #2 number of paired peaks: 352 WARNING @ Sat, 27 Jun 2020 01:01:54: Fewer paired peaks (352) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 352 pairs to build model! INFO @ Sat, 27 Jun 2020 01:01:54: start model_add_line... INFO @ Sat, 27 Jun 2020 01:01:55: start X-correlation... INFO @ Sat, 27 Jun 2020 01:01:55: end of X-cor INFO @ Sat, 27 Jun 2020 01:01:55: #2 finished! INFO @ Sat, 27 Jun 2020 01:01:55: #2 predicted fragment length is 83 bps INFO @ Sat, 27 Jun 2020 01:01:55: #2 alternative fragment length(s) may be 83 bps INFO @ Sat, 27 Jun 2020 01:01:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085369/SRX4085369.05_model.r WARNING @ Sat, 27 Jun 2020 01:01:55: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 01:01:55: #2 You may need to consider one of the other alternative d(s): 83 WARNING @ Sat, 27 Jun 2020 01:01:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 01:01:55: #3 Call peaks... INFO @ Sat, 27 Jun 2020 01:01:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 01:01:55: 19000000 INFO @ Sat, 27 Jun 2020 01:01:57: 25000000 INFO @ Sat, 27 Jun 2020 01:02:04: 20000000 INFO @ Sat, 27 Jun 2020 01:02:04: 26000000 INFO @ Sat, 27 Jun 2020 01:02:12: 27000000 INFO @ Sat, 27 Jun 2020 01:02:13: 21000000 INFO @ Sat, 27 Jun 2020 01:02:14: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 01:02:18: #1 tag size is determined as 51 bps INFO @ Sat, 27 Jun 2020 01:02:18: #1 tag size = 51 INFO @ Sat, 27 Jun 2020 01:02:18: #1 total tags in treatment: 12159013 INFO @ Sat, 27 Jun 2020 01:02:18: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 01:02:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 01:02:18: #1 tags after filtering in treatment: 10404909 INFO @ Sat, 27 Jun 2020 01:02:18: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 27 Jun 2020 01:02:18: #1 finished! INFO @ Sat, 27 Jun 2020 01:02:18: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 01:02:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 01:02:19: #2 number of paired peaks: 352 WARNING @ Sat, 27 Jun 2020 01:02:19: Fewer paired peaks (352) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 352 pairs to build model! INFO @ Sat, 27 Jun 2020 01:02:19: start model_add_line... INFO @ Sat, 27 Jun 2020 01:02:19: start X-correlation... INFO @ Sat, 27 Jun 2020 01:02:19: end of X-cor INFO @ Sat, 27 Jun 2020 01:02:19: #2 finished! INFO @ Sat, 27 Jun 2020 01:02:19: #2 predicted fragment length is 83 bps INFO @ Sat, 27 Jun 2020 01:02:19: #2 alternative fragment length(s) may be 83 bps INFO @ Sat, 27 Jun 2020 01:02:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085369/SRX4085369.10_model.r WARNING @ Sat, 27 Jun 2020 01:02:19: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 01:02:19: #2 You may need to consider one of the other alternative d(s): 83 WARNING @ Sat, 27 Jun 2020 01:02:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 01:02:19: #3 Call peaks... INFO @ Sat, 27 Jun 2020 01:02:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 01:02:23: 22000000 INFO @ Sat, 27 Jun 2020 01:02:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085369/SRX4085369.05_peaks.xls INFO @ Sat, 27 Jun 2020 01:02:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085369/SRX4085369.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 01:02:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085369/SRX4085369.05_summits.bed INFO @ Sat, 27 Jun 2020 01:02:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4495 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 01:02:32: 23000000 INFO @ Sat, 27 Jun 2020 01:02:39: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 01:02:41: 24000000 INFO @ Sat, 27 Jun 2020 01:02:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085369/SRX4085369.10_peaks.xls INFO @ Sat, 27 Jun 2020 01:02:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085369/SRX4085369.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 01:02:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085369/SRX4085369.10_summits.bed INFO @ Sat, 27 Jun 2020 01:02:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2626 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 01:02:50: 25000000 INFO @ Sat, 27 Jun 2020 01:02:59: 26000000 INFO @ Sat, 27 Jun 2020 01:03:07: 27000000 INFO @ Sat, 27 Jun 2020 01:03:15: #1 tag size is determined as 51 bps INFO @ Sat, 27 Jun 2020 01:03:15: #1 tag size = 51 INFO @ Sat, 27 Jun 2020 01:03:15: #1 total tags in treatment: 12159013 INFO @ Sat, 27 Jun 2020 01:03:15: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 01:03:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 01:03:15: #1 tags after filtering in treatment: 10404909 INFO @ Sat, 27 Jun 2020 01:03:15: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 27 Jun 2020 01:03:15: #1 finished! INFO @ Sat, 27 Jun 2020 01:03:15: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 01:03:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 01:03:16: #2 number of paired peaks: 352 WARNING @ Sat, 27 Jun 2020 01:03:16: Fewer paired peaks (352) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 352 pairs to build model! INFO @ Sat, 27 Jun 2020 01:03:16: start model_add_line... INFO @ Sat, 27 Jun 2020 01:03:16: start X-correlation... INFO @ Sat, 27 Jun 2020 01:03:16: end of X-cor INFO @ Sat, 27 Jun 2020 01:03:16: #2 finished! INFO @ Sat, 27 Jun 2020 01:03:16: #2 predicted fragment length is 83 bps INFO @ Sat, 27 Jun 2020 01:03:16: #2 alternative fragment length(s) may be 83 bps INFO @ Sat, 27 Jun 2020 01:03:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085369/SRX4085369.20_model.r WARNING @ Sat, 27 Jun 2020 01:03:16: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 01:03:16: #2 You may need to consider one of the other alternative d(s): 83 WARNING @ Sat, 27 Jun 2020 01:03:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 01:03:16: #3 Call peaks... INFO @ Sat, 27 Jun 2020 01:03:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 01:03:35: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 01:03:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085369/SRX4085369.20_peaks.xls INFO @ Sat, 27 Jun 2020 01:03:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085369/SRX4085369.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 01:03:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085369/SRX4085369.20_summits.bed INFO @ Sat, 27 Jun 2020 01:03:45: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1117 records, 4 fields): 4 millis CompletedMACS2peakCalling