Job ID = 6367818 SRX = SRX4085386 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:43:29 prefetch.2.10.7: 1) Downloading 'SRR7167415'... 2020-06-15T23:43:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:50:07 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:50:07 prefetch.2.10.7: 1) 'SRR7167415' was downloaded successfully Read 20259317 spots for SRR7167415/SRR7167415.sra Written 20259317 spots for SRR7167415/SRR7167415.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: 00:13:06 20259317 reads; of these: 20259317 (100.00%) were paired; of these: 7397472 (36.51%) aligned concordantly 0 times 10955067 (54.07%) aligned concordantly exactly 1 time 1906778 (9.41%) aligned concordantly >1 times ---- 7397472 pairs aligned concordantly 0 times; of these: 451817 (6.11%) aligned discordantly 1 time ---- 6945655 pairs aligned 0 times concordantly or discordantly; of these: 13891310 mates make up the pairs; of these: 9784329 (70.43%) aligned 0 times 3577351 (25.75%) aligned exactly 1 time 529630 (3.81%) aligned >1 times 75.85% overall alignment rate Time searching: 00:13:06 Overall time: 00:13:06 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] 1038157 / 13124483 = 0.0791 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 09:13:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085386/SRX4085386.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085386/SRX4085386.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085386/SRX4085386.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085386/SRX4085386.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 09:13:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:13:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:13:21: 1000000 INFO @ Tue, 16 Jun 2020 09:13:27: 2000000 INFO @ Tue, 16 Jun 2020 09:13:32: 3000000 INFO @ Tue, 16 Jun 2020 09:13:37: 4000000 INFO @ Tue, 16 Jun 2020 09:13:42: 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 09:13:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085386/SRX4085386.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085386/SRX4085386.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085386/SRX4085386.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085386/SRX4085386.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 09:13:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:13:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:13:48: 6000000 INFO @ Tue, 16 Jun 2020 09:13:52: 1000000 INFO @ Tue, 16 Jun 2020 09:13:54: 7000000 INFO @ Tue, 16 Jun 2020 09:13:58: 2000000 INFO @ Tue, 16 Jun 2020 09:14:01: 8000000 INFO @ Tue, 16 Jun 2020 09:14:06: 3000000 INFO @ Tue, 16 Jun 2020 09:14:07: 9000000 INFO @ Tue, 16 Jun 2020 09:14:13: 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 09:14:13: 10000000 INFO @ Tue, 16 Jun 2020 09:14:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085386/SRX4085386.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085386/SRX4085386.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085386/SRX4085386.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085386/SRX4085386.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 09:14:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:14:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:14:20: 11000000 INFO @ Tue, 16 Jun 2020 09:14:20: 5000000 INFO @ Tue, 16 Jun 2020 09:14:21: 1000000 INFO @ Tue, 16 Jun 2020 09:14:26: 12000000 INFO @ Tue, 16 Jun 2020 09:14:27: 6000000 INFO @ Tue, 16 Jun 2020 09:14:28: 2000000 INFO @ Tue, 16 Jun 2020 09:14:33: 13000000 INFO @ Tue, 16 Jun 2020 09:14:34: 7000000 INFO @ Tue, 16 Jun 2020 09:14:34: 3000000 INFO @ Tue, 16 Jun 2020 09:14:39: 14000000 INFO @ Tue, 16 Jun 2020 09:14:41: 4000000 INFO @ Tue, 16 Jun 2020 09:14:41: 8000000 INFO @ Tue, 16 Jun 2020 09:14:46: 15000000 INFO @ Tue, 16 Jun 2020 09:14:47: 5000000 INFO @ Tue, 16 Jun 2020 09:14:48: 9000000 INFO @ Tue, 16 Jun 2020 09:14:52: 16000000 INFO @ Tue, 16 Jun 2020 09:14:54: 6000000 INFO @ Tue, 16 Jun 2020 09:14:55: 10000000 INFO @ Tue, 16 Jun 2020 09:14:59: 17000000 INFO @ Tue, 16 Jun 2020 09:15:01: 7000000 INFO @ Tue, 16 Jun 2020 09:15:02: 11000000 INFO @ Tue, 16 Jun 2020 09:15:06: 18000000 INFO @ Tue, 16 Jun 2020 09:15:07: 8000000 INFO @ Tue, 16 Jun 2020 09:15:10: 12000000 INFO @ Tue, 16 Jun 2020 09:15:12: 19000000 INFO @ Tue, 16 Jun 2020 09:15:14: 9000000 INFO @ Tue, 16 Jun 2020 09:15:16: 13000000 INFO @ Tue, 16 Jun 2020 09:15:19: 20000000 INFO @ Tue, 16 Jun 2020 09:15:20: 10000000 INFO @ Tue, 16 Jun 2020 09:15:23: 14000000 INFO @ Tue, 16 Jun 2020 09:15:26: 21000000 INFO @ Tue, 16 Jun 2020 09:15:27: 11000000 INFO @ Tue, 16 Jun 2020 09:15:30: 15000000 INFO @ Tue, 16 Jun 2020 09:15:32: 22000000 INFO @ Tue, 16 Jun 2020 09:15:33: 12000000 INFO @ Tue, 16 Jun 2020 09:15:37: 16000000 INFO @ Tue, 16 Jun 2020 09:15:39: 23000000 INFO @ Tue, 16 Jun 2020 09:15:40: 13000000 INFO @ Tue, 16 Jun 2020 09:15:44: 17000000 INFO @ Tue, 16 Jun 2020 09:15:45: 24000000 INFO @ Tue, 16 Jun 2020 09:15:46: 14000000 INFO @ Tue, 16 Jun 2020 09:15:51: 18000000 INFO @ Tue, 16 Jun 2020 09:15:52: 25000000 INFO @ Tue, 16 Jun 2020 09:15:53: 15000000 INFO @ Tue, 16 Jun 2020 09:15:58: 19000000 INFO @ Tue, 16 Jun 2020 09:15:59: 26000000 INFO @ Tue, 16 Jun 2020 09:15:59: 16000000 INFO @ Tue, 16 Jun 2020 09:16:05: 27000000 INFO @ Tue, 16 Jun 2020 09:16:05: 20000000 INFO @ Tue, 16 Jun 2020 09:16:06: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:16:12: 28000000 INFO @ Tue, 16 Jun 2020 09:16:12: 18000000 INFO @ Tue, 16 Jun 2020 09:16:12: 21000000 INFO @ Tue, 16 Jun 2020 09:16:16: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:16:16: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:16:16: #1 total tags in treatment: 11843197 INFO @ Tue, 16 Jun 2020 09:16:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:16:16: #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 09:16:16: #1 tags after filtering in treatment: 10203029 INFO @ Tue, 16 Jun 2020 09:16:16: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 16 Jun 2020 09:16:16: #1 finished! INFO @ Tue, 16 Jun 2020 09:16:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:16:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:16:17: #2 number of paired peaks: 276 WARNING @ Tue, 16 Jun 2020 09:16:17: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Tue, 16 Jun 2020 09:16:17: start model_add_line... INFO @ Tue, 16 Jun 2020 09:16:17: start X-correlation... INFO @ Tue, 16 Jun 2020 09:16:17: end of X-cor INFO @ Tue, 16 Jun 2020 09:16:17: #2 finished! INFO @ Tue, 16 Jun 2020 09:16:17: #2 predicted fragment length is 78 bps INFO @ Tue, 16 Jun 2020 09:16:17: #2 alternative fragment length(s) may be 4,78,590,595 bps INFO @ Tue, 16 Jun 2020 09:16:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085386/SRX4085386.05_model.r WARNING @ Tue, 16 Jun 2020 09:16:17: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:16:17: #2 You may need to consider one of the other alternative d(s): 4,78,590,595 WARNING @ Tue, 16 Jun 2020 09:16:17: #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 09:16:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:16:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:16:19: 19000000 INFO @ Tue, 16 Jun 2020 09:16:19: 22000000 INFO @ Tue, 16 Jun 2020 09:16:25: 20000000 INFO @ Tue, 16 Jun 2020 09:16:26: 23000000 INFO @ Tue, 16 Jun 2020 09:16:31: 21000000 INFO @ Tue, 16 Jun 2020 09:16:33: 24000000 INFO @ Tue, 16 Jun 2020 09:16:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:16:38: 22000000 INFO @ Tue, 16 Jun 2020 09:16:40: 25000000 INFO @ Tue, 16 Jun 2020 09:16:44: 23000000 INFO @ Tue, 16 Jun 2020 09:16:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085386/SRX4085386.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:16:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085386/SRX4085386.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:16:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085386/SRX4085386.05_summits.bed INFO @ Tue, 16 Jun 2020 09:16:47: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (2385 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:16:47: 26000000 INFO @ Tue, 16 Jun 2020 09:16:51: 24000000 INFO @ Tue, 16 Jun 2020 09:16:54: 27000000 INFO @ Tue, 16 Jun 2020 09:16:57: 25000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:17:01: 28000000 INFO @ Tue, 16 Jun 2020 09:17:04: 26000000 INFO @ Tue, 16 Jun 2020 09:17:05: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:17:05: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:17:05: #1 total tags in treatment: 11843197 INFO @ Tue, 16 Jun 2020 09:17:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:17:05: #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 09:17:05: #1 tags after filtering in treatment: 10203029 INFO @ Tue, 16 Jun 2020 09:17:05: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 16 Jun 2020 09:17:05: #1 finished! INFO @ Tue, 16 Jun 2020 09:17:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:17:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:17:06: #2 number of paired peaks: 276 WARNING @ Tue, 16 Jun 2020 09:17:06: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Tue, 16 Jun 2020 09:17:06: start model_add_line... INFO @ Tue, 16 Jun 2020 09:17:06: start X-correlation... INFO @ Tue, 16 Jun 2020 09:17:06: end of X-cor INFO @ Tue, 16 Jun 2020 09:17:06: #2 finished! INFO @ Tue, 16 Jun 2020 09:17:06: #2 predicted fragment length is 78 bps INFO @ Tue, 16 Jun 2020 09:17:06: #2 alternative fragment length(s) may be 4,78,590,595 bps INFO @ Tue, 16 Jun 2020 09:17:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085386/SRX4085386.10_model.r WARNING @ Tue, 16 Jun 2020 09:17:06: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:17:06: #2 You may need to consider one of the other alternative d(s): 4,78,590,595 WARNING @ Tue, 16 Jun 2020 09:17:06: #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 09:17:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:17:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:17:09: 27000000 INFO @ Tue, 16 Jun 2020 09:17:14: 28000000 INFO @ Tue, 16 Jun 2020 09:17:18: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:17:18: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:17:18: #1 total tags in treatment: 11843197 INFO @ Tue, 16 Jun 2020 09:17:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:17:18: #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 09:17:18: #1 tags after filtering in treatment: 10203029 INFO @ Tue, 16 Jun 2020 09:17:18: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 16 Jun 2020 09:17:18: #1 finished! INFO @ Tue, 16 Jun 2020 09:17:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:17:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:17:19: #2 number of paired peaks: 276 WARNING @ Tue, 16 Jun 2020 09:17:19: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Tue, 16 Jun 2020 09:17:19: start model_add_line... INFO @ Tue, 16 Jun 2020 09:17:19: start X-correlation... INFO @ Tue, 16 Jun 2020 09:17:19: end of X-cor INFO @ Tue, 16 Jun 2020 09:17:19: #2 finished! INFO @ Tue, 16 Jun 2020 09:17:19: #2 predicted fragment length is 78 bps INFO @ Tue, 16 Jun 2020 09:17:19: #2 alternative fragment length(s) may be 4,78,590,595 bps INFO @ Tue, 16 Jun 2020 09:17:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085386/SRX4085386.20_model.r WARNING @ Tue, 16 Jun 2020 09:17:19: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:17:19: #2 You may need to consider one of the other alternative d(s): 4,78,590,595 WARNING @ Tue, 16 Jun 2020 09:17:19: #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 09:17:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:17:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:17:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:17:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085386/SRX4085386.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:17:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085386/SRX4085386.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:17:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085386/SRX4085386.10_summits.bed INFO @ Tue, 16 Jun 2020 09:17:35: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1232 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:17:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:17:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085386/SRX4085386.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:17:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085386/SRX4085386.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:17:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085386/SRX4085386.20_summits.bed INFO @ Tue, 16 Jun 2020 09:17:48: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (394 records, 4 fields): 1 millis CompletedMACS2peakCalling