Job ID = 14519608 SRX = SRX6581720 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 24393691 spots for SRR9825053/SRR9825053.sra Written 24393691 spots for SRR9825053/SRR9825053.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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:37:41 24393691 reads; of these: 24393691 (100.00%) were unpaired; of these: 696459 (2.86%) aligned 0 times 17233853 (70.65%) aligned exactly 1 time 6463379 (26.50%) aligned >1 times 97.14% overall alignment rate Time searching: 00:37:45 Overall time: 00:37:45 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] 2060490 / 23697232 = 0.0870 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 17:26:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6581720/SRX6581720.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6581720/SRX6581720.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6581720/SRX6581720.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6581720/SRX6581720.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 @ Sat, 15 Jan 2022 17:26:47: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:26:47: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:26:52: 1000000 INFO @ Sat, 15 Jan 2022 17:26:58: 2000000 INFO @ Sat, 15 Jan 2022 17:27:03: 3000000 INFO @ Sat, 15 Jan 2022 17:27:08: 4000000 INFO @ Sat, 15 Jan 2022 17:27:13: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 17:27:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6581720/SRX6581720.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6581720/SRX6581720.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6581720/SRX6581720.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6581720/SRX6581720.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 @ Sat, 15 Jan 2022 17:27:17: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:27:17: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:27:18: 6000000 INFO @ Sat, 15 Jan 2022 17:27:23: 1000000 INFO @ Sat, 15 Jan 2022 17:27:24: 7000000 INFO @ Sat, 15 Jan 2022 17:27:28: 2000000 INFO @ Sat, 15 Jan 2022 17:27:29: 8000000 INFO @ Sat, 15 Jan 2022 17:27:33: 3000000 INFO @ Sat, 15 Jan 2022 17:27:34: 9000000 INFO @ Sat, 15 Jan 2022 17:27:39: 4000000 INFO @ Sat, 15 Jan 2022 17:27:40: 10000000 INFO @ Sat, 15 Jan 2022 17:27:44: 5000000 INFO @ Sat, 15 Jan 2022 17:27:45: 11000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 17:27:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6581720/SRX6581720.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6581720/SRX6581720.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6581720/SRX6581720.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6581720/SRX6581720.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 @ Sat, 15 Jan 2022 17:27:47: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:27:47: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:27:49: 6000000 INFO @ Sat, 15 Jan 2022 17:27:50: 12000000 INFO @ Sat, 15 Jan 2022 17:27:54: 1000000 INFO @ Sat, 15 Jan 2022 17:27:54: 7000000 INFO @ Sat, 15 Jan 2022 17:27:56: 13000000 INFO @ Sat, 15 Jan 2022 17:28:00: 2000000 INFO @ Sat, 15 Jan 2022 17:28:00: 8000000 INFO @ Sat, 15 Jan 2022 17:28:01: 14000000 INFO @ Sat, 15 Jan 2022 17:28:05: 9000000 INFO @ Sat, 15 Jan 2022 17:28:05: 3000000 INFO @ Sat, 15 Jan 2022 17:28:06: 15000000 INFO @ Sat, 15 Jan 2022 17:28:11: 10000000 INFO @ Sat, 15 Jan 2022 17:28:11: 4000000 INFO @ Sat, 15 Jan 2022 17:28:12: 16000000 INFO @ Sat, 15 Jan 2022 17:28:16: 11000000 INFO @ Sat, 15 Jan 2022 17:28:16: 5000000 INFO @ Sat, 15 Jan 2022 17:28:17: 17000000 INFO @ Sat, 15 Jan 2022 17:28:21: 12000000 INFO @ Sat, 15 Jan 2022 17:28:22: 6000000 INFO @ Sat, 15 Jan 2022 17:28:22: 18000000 INFO @ Sat, 15 Jan 2022 17:28:27: 13000000 INFO @ Sat, 15 Jan 2022 17:28:28: 19000000 INFO @ Sat, 15 Jan 2022 17:28:29: 7000000 INFO @ Sat, 15 Jan 2022 17:28:32: 14000000 INFO @ Sat, 15 Jan 2022 17:28:33: 20000000 INFO @ Sat, 15 Jan 2022 17:28:35: 8000000 INFO @ Sat, 15 Jan 2022 17:28:37: 15000000 INFO @ Sat, 15 Jan 2022 17:28:39: 21000000 INFO @ Sat, 15 Jan 2022 17:28:41: 9000000 INFO @ Sat, 15 Jan 2022 17:28:42: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 17:28:42: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 17:28:42: #1 total tags in treatment: 21636742 INFO @ Sat, 15 Jan 2022 17:28:42: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:28:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 17:28:43: 16000000 INFO @ Sat, 15 Jan 2022 17:28:43: #1 tags after filtering in treatment: 21636627 INFO @ Sat, 15 Jan 2022 17:28:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:28:43: #1 finished! INFO @ Sat, 15 Jan 2022 17:28:43: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:28:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:28:45: #2 number of paired peaks: 4912 INFO @ Sat, 15 Jan 2022 17:28:45: start model_add_line... INFO @ Sat, 15 Jan 2022 17:28:45: start X-correlation... INFO @ Sat, 15 Jan 2022 17:28:45: end of X-cor INFO @ Sat, 15 Jan 2022 17:28:45: #2 finished! INFO @ Sat, 15 Jan 2022 17:28:45: #2 predicted fragment length is 75 bps INFO @ Sat, 15 Jan 2022 17:28:45: #2 alternative fragment length(s) may be 75,517 bps INFO @ Sat, 15 Jan 2022 17:28:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6581720/SRX6581720.05_model.r WARNING @ Sat, 15 Jan 2022 17:28:45: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 17:28:45: #2 You may need to consider one of the other alternative d(s): 75,517 WARNING @ Sat, 15 Jan 2022 17:28:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 17:28:45: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:28:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:28:47: 10000000 INFO @ Sat, 15 Jan 2022 17:28:48: 17000000 INFO @ Sat, 15 Jan 2022 17:28:53: 11000000 INFO @ Sat, 15 Jan 2022 17:28:53: 18000000 INFO @ Sat, 15 Jan 2022 17:28:59: 12000000 INFO @ Sat, 15 Jan 2022 17:28:59: 19000000 INFO @ Sat, 15 Jan 2022 17:29:04: 20000000 INFO @ Sat, 15 Jan 2022 17:29:04: 13000000 INFO @ Sat, 15 Jan 2022 17:29:10: 21000000 INFO @ Sat, 15 Jan 2022 17:29:10: 14000000 INFO @ Sat, 15 Jan 2022 17:29:13: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 17:29:13: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 17:29:13: #1 total tags in treatment: 21636742 INFO @ Sat, 15 Jan 2022 17:29:13: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:29:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 17:29:14: #1 tags after filtering in treatment: 21636627 INFO @ Sat, 15 Jan 2022 17:29:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:29:14: #1 finished! INFO @ Sat, 15 Jan 2022 17:29:14: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:29:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:29:16: #2 number of paired peaks: 4912 INFO @ Sat, 15 Jan 2022 17:29:16: start model_add_line... INFO @ Sat, 15 Jan 2022 17:29:16: start X-correlation... INFO @ Sat, 15 Jan 2022 17:29:16: end of X-cor INFO @ Sat, 15 Jan 2022 17:29:16: #2 finished! INFO @ Sat, 15 Jan 2022 17:29:16: #2 predicted fragment length is 75 bps INFO @ Sat, 15 Jan 2022 17:29:16: #2 alternative fragment length(s) may be 75,517 bps INFO @ Sat, 15 Jan 2022 17:29:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6581720/SRX6581720.10_model.r WARNING @ Sat, 15 Jan 2022 17:29:16: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 17:29:16: #2 You may need to consider one of the other alternative d(s): 75,517 WARNING @ Sat, 15 Jan 2022 17:29:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 17:29:16: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:29:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:29:16: 15000000 INFO @ Sat, 15 Jan 2022 17:29:22: 16000000 INFO @ Sat, 15 Jan 2022 17:29:28: 17000000 INFO @ Sat, 15 Jan 2022 17:29:32: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:29:34: 18000000 INFO @ Sat, 15 Jan 2022 17:29:40: 19000000 INFO @ Sat, 15 Jan 2022 17:29:46: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 17:29:52: 21000000 INFO @ Sat, 15 Jan 2022 17:29:56: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 17:29:56: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 17:29:56: #1 total tags in treatment: 21636742 INFO @ Sat, 15 Jan 2022 17:29:56: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:29:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 17:29:56: #1 tags after filtering in treatment: 21636627 INFO @ Sat, 15 Jan 2022 17:29:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:29:56: #1 finished! INFO @ Sat, 15 Jan 2022 17:29:56: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:29:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:29:56: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6581720/SRX6581720.05_peaks.xls INFO @ Sat, 15 Jan 2022 17:29:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6581720/SRX6581720.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:29:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6581720/SRX6581720.05_summits.bed INFO @ Sat, 15 Jan 2022 17:29:56: Done! pass1 - making usageList (45 chroms): 1 millis pass2 - checking and writing primary data (1324 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:29:58: #2 number of paired peaks: 4912 INFO @ Sat, 15 Jan 2022 17:29:58: start model_add_line... INFO @ Sat, 15 Jan 2022 17:29:58: start X-correlation... INFO @ Sat, 15 Jan 2022 17:29:58: end of X-cor INFO @ Sat, 15 Jan 2022 17:29:58: #2 finished! INFO @ Sat, 15 Jan 2022 17:29:58: #2 predicted fragment length is 75 bps INFO @ Sat, 15 Jan 2022 17:29:58: #2 alternative fragment length(s) may be 75,517 bps INFO @ Sat, 15 Jan 2022 17:29:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6581720/SRX6581720.20_model.r WARNING @ Sat, 15 Jan 2022 17:29:58: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 17:29:58: #2 You may need to consider one of the other alternative d(s): 75,517 WARNING @ Sat, 15 Jan 2022 17:29:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 17:29:58: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:29:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:30:02: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:30:26: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6581720/SRX6581720.10_peaks.xls INFO @ Sat, 15 Jan 2022 17:30:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6581720/SRX6581720.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:30:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6581720/SRX6581720.10_summits.bed INFO @ Sat, 15 Jan 2022 17:30:26: Done! pass1 - making usageList (40 chroms): 1 millis pass2 - checking and writing primary data (789 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 17:30:46: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:31:10: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6581720/SRX6581720.20_peaks.xls INFO @ Sat, 15 Jan 2022 17:31:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6581720/SRX6581720.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:31:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6581720/SRX6581720.20_summits.bed INFO @ Sat, 15 Jan 2022 17:31:10: Done! pass1 - making usageList (30 chroms): 0 millis pass2 - checking and writing primary data (436 records, 4 fields): 3 millis CompletedMACS2peakCalling