Job ID = 7097186 SRX = SRX6922978 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 29309499 spots for SRR10202924/SRR10202924.sra Written 29309499 spots for SRR10202924/SRR10202924.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:43:24 29309499 reads; of these: 29309499 (100.00%) were unpaired; of these: 1015198 (3.46%) aligned 0 times 25259943 (86.18%) aligned exactly 1 time 3034358 (10.35%) aligned >1 times 96.54% overall alignment rate Time searching: 00:43:27 Overall time: 00:43:27 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 4142855 / 28294301 = 0.1464 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 @ Wed, 22 Jul 2020 12:12:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6922978/SRX6922978.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6922978/SRX6922978.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6922978/SRX6922978.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6922978/SRX6922978.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Jul 2020 12:12:32: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:12:32: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:12:39: 1000000 INFO @ Wed, 22 Jul 2020 12:12:46: 2000000 INFO @ Wed, 22 Jul 2020 12:12:53: 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 @ Wed, 22 Jul 2020 12:13:00: 4000000 INFO @ Wed, 22 Jul 2020 12:13:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6922978/SRX6922978.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6922978/SRX6922978.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6922978/SRX6922978.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6922978/SRX6922978.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Jul 2020 12:13:02: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:13:02: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:13:08: 5000000 INFO @ Wed, 22 Jul 2020 12:13:09: 1000000 INFO @ Wed, 22 Jul 2020 12:13:15: 6000000 INFO @ Wed, 22 Jul 2020 12:13:17: 2000000 INFO @ Wed, 22 Jul 2020 12:13:23: 7000000 INFO @ Wed, 22 Jul 2020 12:13:25: 3000000 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 @ Wed, 22 Jul 2020 12:13:30: 8000000 INFO @ Wed, 22 Jul 2020 12:13:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6922978/SRX6922978.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6922978/SRX6922978.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6922978/SRX6922978.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6922978/SRX6922978.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Jul 2020 12:13:32: #1 read tag files... INFO @ Wed, 22 Jul 2020 12:13:32: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 12:13:33: 4000000 INFO @ Wed, 22 Jul 2020 12:13:38: 9000000 INFO @ Wed, 22 Jul 2020 12:13:39: 1000000 INFO @ Wed, 22 Jul 2020 12:13:40: 5000000 INFO @ Wed, 22 Jul 2020 12:13:46: 10000000 INFO @ Wed, 22 Jul 2020 12:13:46: 2000000 INFO @ Wed, 22 Jul 2020 12:13:48: 6000000 INFO @ Wed, 22 Jul 2020 12:13:53: 3000000 INFO @ Wed, 22 Jul 2020 12:13:53: 11000000 INFO @ Wed, 22 Jul 2020 12:13:56: 7000000 INFO @ Wed, 22 Jul 2020 12:14:00: 4000000 INFO @ Wed, 22 Jul 2020 12:14:01: 12000000 INFO @ Wed, 22 Jul 2020 12:14:04: 8000000 INFO @ Wed, 22 Jul 2020 12:14:07: 5000000 INFO @ Wed, 22 Jul 2020 12:14:09: 13000000 INFO @ Wed, 22 Jul 2020 12:14:12: 9000000 INFO @ Wed, 22 Jul 2020 12:14:14: 6000000 INFO @ Wed, 22 Jul 2020 12:14:16: 14000000 INFO @ Wed, 22 Jul 2020 12:14:19: 10000000 INFO @ Wed, 22 Jul 2020 12:14:21: 7000000 INFO @ Wed, 22 Jul 2020 12:14:24: 15000000 INFO @ Wed, 22 Jul 2020 12:14:27: 11000000 INFO @ Wed, 22 Jul 2020 12:14:28: 8000000 INFO @ Wed, 22 Jul 2020 12:14:32: 16000000 INFO @ Wed, 22 Jul 2020 12:14:35: 12000000 INFO @ Wed, 22 Jul 2020 12:14:35: 9000000 INFO @ Wed, 22 Jul 2020 12:14:39: 17000000 INFO @ Wed, 22 Jul 2020 12:14:42: 10000000 INFO @ Wed, 22 Jul 2020 12:14:43: 13000000 INFO @ Wed, 22 Jul 2020 12:14:47: 18000000 INFO @ Wed, 22 Jul 2020 12:14:49: 11000000 INFO @ Wed, 22 Jul 2020 12:14:51: 14000000 INFO @ Wed, 22 Jul 2020 12:14:55: 19000000 INFO @ Wed, 22 Jul 2020 12:14:56: 12000000 INFO @ Wed, 22 Jul 2020 12:14:58: 15000000 INFO @ Wed, 22 Jul 2020 12:15:02: 20000000 INFO @ Wed, 22 Jul 2020 12:15:03: 13000000 INFO @ Wed, 22 Jul 2020 12:15:06: 16000000 INFO @ Wed, 22 Jul 2020 12:15:10: 21000000 INFO @ Wed, 22 Jul 2020 12:15:10: 14000000 INFO @ Wed, 22 Jul 2020 12:15:14: 17000000 INFO @ Wed, 22 Jul 2020 12:15:17: 15000000 INFO @ Wed, 22 Jul 2020 12:15:17: 22000000 INFO @ Wed, 22 Jul 2020 12:15:22: 18000000 INFO @ Wed, 22 Jul 2020 12:15:24: 16000000 INFO @ Wed, 22 Jul 2020 12:15:25: 23000000 INFO @ Wed, 22 Jul 2020 12:15:29: 19000000 INFO @ Wed, 22 Jul 2020 12:15:31: 17000000 INFO @ Wed, 22 Jul 2020 12:15:33: 24000000 INFO @ Wed, 22 Jul 2020 12:15:34: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 12:15:34: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 12:15:34: #1 total tags in treatment: 24151446 INFO @ Wed, 22 Jul 2020 12:15:34: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:15:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 12:15:35: #1 tags after filtering in treatment: 24151224 INFO @ Wed, 22 Jul 2020 12:15:35: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 12:15:35: #1 finished! INFO @ Wed, 22 Jul 2020 12:15:35: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:15:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 12:15:37: 20000000 INFO @ Wed, 22 Jul 2020 12:15:38: 18000000 INFO @ Wed, 22 Jul 2020 12:15:39: #2 number of paired peaks: 94001 INFO @ Wed, 22 Jul 2020 12:15:39: start model_add_line... INFO @ Wed, 22 Jul 2020 12:15:40: start X-correlation... INFO @ Wed, 22 Jul 2020 12:15:40: end of X-cor INFO @ Wed, 22 Jul 2020 12:15:40: #2 finished! INFO @ Wed, 22 Jul 2020 12:15:40: #2 predicted fragment length is 147 bps INFO @ Wed, 22 Jul 2020 12:15:40: #2 alternative fragment length(s) may be 147 bps INFO @ Wed, 22 Jul 2020 12:15:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6922978/SRX6922978.05_model.r WARNING @ Wed, 22 Jul 2020 12:15:40: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 12:15:40: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Wed, 22 Jul 2020 12:15:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Jul 2020 12:15:40: #3 Call peaks... INFO @ Wed, 22 Jul 2020 12:15:40: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 12:15:45: 19000000 INFO @ Wed, 22 Jul 2020 12:15:45: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 12:15:51: 20000000 INFO @ Wed, 22 Jul 2020 12:15:52: 22000000 INFO @ Wed, 22 Jul 2020 12:15:58: 21000000 INFO @ Wed, 22 Jul 2020 12:16:01: 23000000 INFO @ Wed, 22 Jul 2020 12:16:05: 22000000 INFO @ Wed, 22 Jul 2020 12:16:08: 24000000 INFO @ Wed, 22 Jul 2020 12:16:10: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 12:16:10: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 12:16:10: #1 total tags in treatment: 24151446 INFO @ Wed, 22 Jul 2020 12:16:10: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:16:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 12:16:10: #1 tags after filtering in treatment: 24151224 INFO @ Wed, 22 Jul 2020 12:16:10: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 12:16:10: #1 finished! INFO @ Wed, 22 Jul 2020 12:16:10: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:16:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 12:16:12: 23000000 INFO @ Wed, 22 Jul 2020 12:16:15: #2 number of paired peaks: 94001 INFO @ Wed, 22 Jul 2020 12:16:15: start model_add_line... INFO @ Wed, 22 Jul 2020 12:16:15: start X-correlation... INFO @ Wed, 22 Jul 2020 12:16:15: end of X-cor INFO @ Wed, 22 Jul 2020 12:16:15: #2 finished! INFO @ Wed, 22 Jul 2020 12:16:15: #2 predicted fragment length is 147 bps INFO @ Wed, 22 Jul 2020 12:16:15: #2 alternative fragment length(s) may be 147 bps INFO @ Wed, 22 Jul 2020 12:16:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6922978/SRX6922978.10_model.r WARNING @ Wed, 22 Jul 2020 12:16:15: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 12:16:15: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Wed, 22 Jul 2020 12:16:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Jul 2020 12:16:15: #3 Call peaks... INFO @ Wed, 22 Jul 2020 12:16:15: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 12:16:18: 24000000 INFO @ Wed, 22 Jul 2020 12:16:19: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 12:16:19: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 12:16:19: #1 total tags in treatment: 24151446 INFO @ Wed, 22 Jul 2020 12:16:19: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 12:16:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 12:16:20: #1 tags after filtering in treatment: 24151224 INFO @ Wed, 22 Jul 2020 12:16:20: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 12:16:20: #1 finished! INFO @ Wed, 22 Jul 2020 12:16:20: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 12:16:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 12:16:24: #2 number of paired peaks: 94001 INFO @ Wed, 22 Jul 2020 12:16:24: start model_add_line... INFO @ Wed, 22 Jul 2020 12:16:25: start X-correlation... INFO @ Wed, 22 Jul 2020 12:16:25: end of X-cor INFO @ Wed, 22 Jul 2020 12:16:25: #2 finished! INFO @ Wed, 22 Jul 2020 12:16:25: #2 predicted fragment length is 147 bps INFO @ Wed, 22 Jul 2020 12:16:25: #2 alternative fragment length(s) may be 147 bps INFO @ Wed, 22 Jul 2020 12:16:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6922978/SRX6922978.20_model.r WARNING @ Wed, 22 Jul 2020 12:16:25: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 12:16:25: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Wed, 22 Jul 2020 12:16:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Jul 2020 12:16:25: #3 Call peaks... INFO @ Wed, 22 Jul 2020 12:16:25: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 12:16:43: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 12:17:16: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 12:17:18: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6922978/SRX6922978.05_peaks.xls INFO @ Wed, 22 Jul 2020 12:17:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6922978/SRX6922978.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 12:17:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6922978/SRX6922978.05_summits.bed INFO @ Wed, 22 Jul 2020 12:17:19: Done! pass1 - making usageList (122 chroms): 8 millis pass2 - checking and writing primary data (53310 records, 4 fields): 50 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 12:17:25: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 12:17:50: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6922978/SRX6922978.10_peaks.xls INFO @ Wed, 22 Jul 2020 12:17:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6922978/SRX6922978.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 12:17:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6922978/SRX6922978.10_summits.bed INFO @ Wed, 22 Jul 2020 12:17:51: Done! pass1 - making usageList (96 chroms): 5 millis pass2 - checking and writing primary data (36318 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 12:17:57: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6922978/SRX6922978.20_peaks.xls INFO @ Wed, 22 Jul 2020 12:17:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6922978/SRX6922978.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 12:17:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6922978/SRX6922978.20_summits.bed INFO @ Wed, 22 Jul 2020 12:17:57: Done! pass1 - making usageList (70 chroms): 3 millis pass2 - checking and writing primary data (21488 records, 4 fields): 21 millis CompletedMACS2peakCalling