Job ID = 6367810 SRX = SRX4085378 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:35:20 prefetch.2.10.7: 1) Downloading 'SRR7167407'... 2020-06-15T23:35:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:45:34 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:45:34 prefetch.2.10.7: 1) 'SRR7167407' was downloaded successfully Read 24712379 spots for SRR7167407/SRR7167407.sra Written 24712379 spots for SRR7167407/SRR7167407.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: 00:15:05 24712379 reads; of these: 24712379 (100.00%) were paired; of these: 14406794 (58.30%) aligned concordantly 0 times 8775185 (35.51%) aligned concordantly exactly 1 time 1530400 (6.19%) aligned concordantly >1 times ---- 14406794 pairs aligned concordantly 0 times; of these: 704937 (4.89%) aligned discordantly 1 time ---- 13701857 pairs aligned 0 times concordantly or discordantly; of these: 27403714 mates make up the pairs; of these: 18588310 (67.83%) aligned 0 times 7785612 (28.41%) aligned exactly 1 time 1029792 (3.76%) aligned >1 times 62.39% overall alignment rate Time searching: 00:15:05 Overall time: 00:15:05 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] 993230 / 10737685 = 0.0925 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 09:12:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085378/SRX4085378.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085378/SRX4085378.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085378/SRX4085378.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085378/SRX4085378.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 09:12:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:12:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:12:39: 1000000 INFO @ Tue, 16 Jun 2020 09:12:45: 2000000 INFO @ Tue, 16 Jun 2020 09:12:52: 3000000 INFO @ Tue, 16 Jun 2020 09:12:58: 4000000 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 09:13:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085378/SRX4085378.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085378/SRX4085378.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085378/SRX4085378.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085378/SRX4085378.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 09:13:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:13:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:13:05: 5000000 INFO @ Tue, 16 Jun 2020 09:13:11: 1000000 INFO @ Tue, 16 Jun 2020 09:13:12: 6000000 INFO @ Tue, 16 Jun 2020 09:13:19: 2000000 INFO @ Tue, 16 Jun 2020 09:13:20: 7000000 INFO @ Tue, 16 Jun 2020 09:13:28: 3000000 INFO @ Tue, 16 Jun 2020 09:13:28: 8000000 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 09:13:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085378/SRX4085378.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085378/SRX4085378.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085378/SRX4085378.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085378/SRX4085378.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 09:13:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:13:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:13:37: 9000000 INFO @ Tue, 16 Jun 2020 09:13:37: 4000000 INFO @ Tue, 16 Jun 2020 09:13:40: 1000000 INFO @ Tue, 16 Jun 2020 09:13:45: 10000000 INFO @ Tue, 16 Jun 2020 09:13:46: 5000000 INFO @ Tue, 16 Jun 2020 09:13:49: 2000000 INFO @ Tue, 16 Jun 2020 09:13:53: 11000000 INFO @ Tue, 16 Jun 2020 09:13:54: 6000000 INFO @ Tue, 16 Jun 2020 09:13:57: 3000000 INFO @ Tue, 16 Jun 2020 09:14:02: 12000000 INFO @ Tue, 16 Jun 2020 09:14:03: 7000000 INFO @ Tue, 16 Jun 2020 09:14:05: 4000000 INFO @ Tue, 16 Jun 2020 09:14:10: 13000000 INFO @ Tue, 16 Jun 2020 09:14:12: 8000000 INFO @ Tue, 16 Jun 2020 09:14:14: 5000000 INFO @ Tue, 16 Jun 2020 09:14:18: 14000000 INFO @ Tue, 16 Jun 2020 09:14:21: 9000000 INFO @ Tue, 16 Jun 2020 09:14:22: 6000000 INFO @ Tue, 16 Jun 2020 09:14:27: 15000000 INFO @ Tue, 16 Jun 2020 09:14:30: 10000000 INFO @ Tue, 16 Jun 2020 09:14:30: 7000000 INFO @ Tue, 16 Jun 2020 09:14:35: 16000000 INFO @ Tue, 16 Jun 2020 09:14:38: 11000000 INFO @ Tue, 16 Jun 2020 09:14:39: 8000000 INFO @ Tue, 16 Jun 2020 09:14:43: 17000000 INFO @ Tue, 16 Jun 2020 09:14:47: 9000000 INFO @ Tue, 16 Jun 2020 09:14:47: 12000000 INFO @ Tue, 16 Jun 2020 09:14:52: 18000000 INFO @ Tue, 16 Jun 2020 09:14:55: 10000000 INFO @ Tue, 16 Jun 2020 09:14:56: 13000000 INFO @ Tue, 16 Jun 2020 09:15:00: 19000000 INFO @ Tue, 16 Jun 2020 09:15:04: 11000000 INFO @ Tue, 16 Jun 2020 09:15:04: 14000000 INFO @ Tue, 16 Jun 2020 09:15:08: 20000000 INFO @ Tue, 16 Jun 2020 09:15:12: 12000000 INFO @ Tue, 16 Jun 2020 09:15:13: 15000000 INFO @ Tue, 16 Jun 2020 09:15:16: 21000000 INFO @ Tue, 16 Jun 2020 09:15:20: 13000000 INFO @ Tue, 16 Jun 2020 09:15:22: 16000000 INFO @ Tue, 16 Jun 2020 09:15:25: 22000000 INFO @ Tue, 16 Jun 2020 09:15:28: 14000000 INFO @ Tue, 16 Jun 2020 09:15:31: 17000000 INFO @ Tue, 16 Jun 2020 09:15:33: 23000000 INFO @ Tue, 16 Jun 2020 09:15:37: 15000000 INFO @ Tue, 16 Jun 2020 09:15:39: 18000000 INFO @ Tue, 16 Jun 2020 09:15:42: 24000000 INFO @ Tue, 16 Jun 2020 09:15:45: 16000000 INFO @ Tue, 16 Jun 2020 09:15:48: 19000000 INFO @ Tue, 16 Jun 2020 09:15:50: 25000000 INFO @ Tue, 16 Jun 2020 09:15:54: 17000000 INFO @ Tue, 16 Jun 2020 09:15:57: 20000000 INFO @ Tue, 16 Jun 2020 09:15:58: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:16:02: 18000000 INFO @ Tue, 16 Jun 2020 09:16:06: 27000000 INFO @ Tue, 16 Jun 2020 09:16:06: 21000000 INFO @ Tue, 16 Jun 2020 09:16:10: 19000000 INFO @ Tue, 16 Jun 2020 09:16:14: 28000000 INFO @ Tue, 16 Jun 2020 09:16:15: 22000000 INFO @ Tue, 16 Jun 2020 09:16:18: 20000000 INFO @ Tue, 16 Jun 2020 09:16:20: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:16:20: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:16:20: #1 total tags in treatment: 9353941 INFO @ Tue, 16 Jun 2020 09:16:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:16:20: #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 09:16:20: #1 tags after filtering in treatment: 8062529 INFO @ Tue, 16 Jun 2020 09:16:20: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 16 Jun 2020 09:16:20: #1 finished! INFO @ Tue, 16 Jun 2020 09:16:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:16:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:16:21: #2 number of paired peaks: 427 WARNING @ Tue, 16 Jun 2020 09:16:21: Fewer paired peaks (427) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 427 pairs to build model! INFO @ Tue, 16 Jun 2020 09:16:21: start model_add_line... INFO @ Tue, 16 Jun 2020 09:16:21: start X-correlation... INFO @ Tue, 16 Jun 2020 09:16:21: end of X-cor INFO @ Tue, 16 Jun 2020 09:16:21: #2 finished! INFO @ Tue, 16 Jun 2020 09:16:21: #2 predicted fragment length is 81 bps INFO @ Tue, 16 Jun 2020 09:16:21: #2 alternative fragment length(s) may be 81 bps INFO @ Tue, 16 Jun 2020 09:16:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085378/SRX4085378.05_model.r WARNING @ Tue, 16 Jun 2020 09:16:21: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:16:21: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Tue, 16 Jun 2020 09:16:21: #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 09:16:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:16:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:16:24: 23000000 INFO @ Tue, 16 Jun 2020 09:16:26: 21000000 INFO @ Tue, 16 Jun 2020 09:16:33: 24000000 INFO @ Tue, 16 Jun 2020 09:16:34: 22000000 INFO @ Tue, 16 Jun 2020 09:16:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:16:41: 23000000 INFO @ Tue, 16 Jun 2020 09:16:42: 25000000 INFO @ Tue, 16 Jun 2020 09:16:49: 24000000 INFO @ Tue, 16 Jun 2020 09:16:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085378/SRX4085378.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:16:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085378/SRX4085378.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:16:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085378/SRX4085378.05_summits.bed INFO @ Tue, 16 Jun 2020 09:16:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4353 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:16:51: 26000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:16:56: 25000000 INFO @ Tue, 16 Jun 2020 09:17:00: 27000000 INFO @ Tue, 16 Jun 2020 09:17:04: 26000000 INFO @ Tue, 16 Jun 2020 09:17:08: 28000000 INFO @ Tue, 16 Jun 2020 09:17:12: 27000000 INFO @ Tue, 16 Jun 2020 09:17:14: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:17:14: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:17:14: #1 total tags in treatment: 9353941 INFO @ Tue, 16 Jun 2020 09:17:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:17:14: #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 09:17:15: #1 tags after filtering in treatment: 8062529 INFO @ Tue, 16 Jun 2020 09:17:15: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 16 Jun 2020 09:17:15: #1 finished! INFO @ Tue, 16 Jun 2020 09:17:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:17:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:17:15: #2 number of paired peaks: 427 WARNING @ Tue, 16 Jun 2020 09:17:15: Fewer paired peaks (427) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 427 pairs to build model! INFO @ Tue, 16 Jun 2020 09:17:15: start model_add_line... INFO @ Tue, 16 Jun 2020 09:17:15: start X-correlation... INFO @ Tue, 16 Jun 2020 09:17:15: end of X-cor INFO @ Tue, 16 Jun 2020 09:17:15: #2 finished! INFO @ Tue, 16 Jun 2020 09:17:15: #2 predicted fragment length is 81 bps INFO @ Tue, 16 Jun 2020 09:17:15: #2 alternative fragment length(s) may be 81 bps INFO @ Tue, 16 Jun 2020 09:17:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085378/SRX4085378.10_model.r WARNING @ Tue, 16 Jun 2020 09:17:15: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:17:15: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Tue, 16 Jun 2020 09:17:15: #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 09:17:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:17:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:17:18: 28000000 INFO @ Tue, 16 Jun 2020 09:17:23: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:17:23: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:17:23: #1 total tags in treatment: 9353941 INFO @ Tue, 16 Jun 2020 09:17:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:17:23: #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 09:17:23: #1 tags after filtering in treatment: 8062529 INFO @ Tue, 16 Jun 2020 09:17:23: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 16 Jun 2020 09:17:23: #1 finished! INFO @ Tue, 16 Jun 2020 09:17:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:17:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:17:24: #2 number of paired peaks: 427 WARNING @ Tue, 16 Jun 2020 09:17:24: Fewer paired peaks (427) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 427 pairs to build model! INFO @ Tue, 16 Jun 2020 09:17:24: start model_add_line... INFO @ Tue, 16 Jun 2020 09:17:24: start X-correlation... INFO @ Tue, 16 Jun 2020 09:17:24: end of X-cor INFO @ Tue, 16 Jun 2020 09:17:24: #2 finished! INFO @ Tue, 16 Jun 2020 09:17:24: #2 predicted fragment length is 81 bps INFO @ Tue, 16 Jun 2020 09:17:24: #2 alternative fragment length(s) may be 81 bps INFO @ Tue, 16 Jun 2020 09:17:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085378/SRX4085378.20_model.r WARNING @ Tue, 16 Jun 2020 09:17:24: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:17:24: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Tue, 16 Jun 2020 09:17:24: #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 09:17:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:17:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:17:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:17:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:17:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085378/SRX4085378.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:17:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085378/SRX4085378.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:17:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085378/SRX4085378.10_summits.bed INFO @ Tue, 16 Jun 2020 09:17:43: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (2450 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:17:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085378/SRX4085378.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:17:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085378/SRX4085378.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:17:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085378/SRX4085378.20_summits.bed INFO @ Tue, 16 Jun 2020 09:17:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1142 records, 4 fields): 2 millis CompletedMACS2peakCalling