Job ID = 6627028 SRX = SRX7351013 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:08:16 22526749 reads; of these: 22526749 (100.00%) were unpaired; of these: 738502 (3.28%) aligned 0 times 15320447 (68.01%) aligned exactly 1 time 6467800 (28.71%) aligned >1 times 96.72% overall alignment rate Time searching: 00:08:16 Overall time: 00:08:16 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 3842049 / 21788247 = 0.1763 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, 14 Jul 2020 09:44:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7351013/SRX7351013.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7351013/SRX7351013.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7351013/SRX7351013.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7351013/SRX7351013.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 14 Jul 2020 09:44:19: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:44:19: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:44:26: 1000000 INFO @ Tue, 14 Jul 2020 09:44:32: 2000000 INFO @ Tue, 14 Jul 2020 09:44:38: 3000000 INFO @ Tue, 14 Jul 2020 09:44:45: 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, 14 Jul 2020 09:44:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7351013/SRX7351013.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7351013/SRX7351013.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7351013/SRX7351013.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7351013/SRX7351013.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 14 Jul 2020 09:44:49: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:44:49: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:44:52: 5000000 INFO @ Tue, 14 Jul 2020 09:44:58: 1000000 INFO @ Tue, 14 Jul 2020 09:45:00: 6000000 INFO @ Tue, 14 Jul 2020 09:45:06: 2000000 INFO @ Tue, 14 Jul 2020 09:45:08: 7000000 INFO @ Tue, 14 Jul 2020 09:45:15: 3000000 INFO @ Tue, 14 Jul 2020 09:45:16: 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, 14 Jul 2020 09:45:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7351013/SRX7351013.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7351013/SRX7351013.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7351013/SRX7351013.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7351013/SRX7351013.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 14 Jul 2020 09:45:19: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:45:19: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:45:24: 4000000 INFO @ Tue, 14 Jul 2020 09:45:25: 9000000 INFO @ Tue, 14 Jul 2020 09:45:31: 1000000 INFO @ Tue, 14 Jul 2020 09:45:32: 5000000 INFO @ Tue, 14 Jul 2020 09:45:33: 10000000 INFO @ Tue, 14 Jul 2020 09:45:39: 2000000 INFO @ Tue, 14 Jul 2020 09:45:41: 11000000 INFO @ Tue, 14 Jul 2020 09:45:41: 6000000 INFO @ Tue, 14 Jul 2020 09:45:47: 3000000 INFO @ Tue, 14 Jul 2020 09:45:49: 12000000 INFO @ Tue, 14 Jul 2020 09:45:50: 7000000 INFO @ Tue, 14 Jul 2020 09:45:55: 4000000 INFO @ Tue, 14 Jul 2020 09:45:57: 13000000 INFO @ Tue, 14 Jul 2020 09:45:58: 8000000 INFO @ Tue, 14 Jul 2020 09:46:03: 5000000 INFO @ Tue, 14 Jul 2020 09:46:05: 14000000 INFO @ Tue, 14 Jul 2020 09:46:07: 9000000 INFO @ Tue, 14 Jul 2020 09:46:12: 6000000 INFO @ Tue, 14 Jul 2020 09:46:13: 15000000 INFO @ Tue, 14 Jul 2020 09:46:16: 10000000 INFO @ Tue, 14 Jul 2020 09:46:20: 7000000 INFO @ Tue, 14 Jul 2020 09:46:22: 16000000 INFO @ Tue, 14 Jul 2020 09:46:24: 11000000 INFO @ Tue, 14 Jul 2020 09:46:28: 8000000 INFO @ Tue, 14 Jul 2020 09:46:30: 17000000 INFO @ Tue, 14 Jul 2020 09:46:33: 12000000 INFO @ Tue, 14 Jul 2020 09:46:36: 9000000 INFO @ Tue, 14 Jul 2020 09:46:38: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 09:46:38: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 09:46:38: #1 total tags in treatment: 17946198 INFO @ Tue, 14 Jul 2020 09:46:38: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:46:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 09:46:39: #1 tags after filtering in treatment: 17946104 INFO @ Tue, 14 Jul 2020 09:46:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:46:39: #1 finished! INFO @ Tue, 14 Jul 2020 09:46:39: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:46:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:46:40: #2 number of paired peaks: 1204 INFO @ Tue, 14 Jul 2020 09:46:40: start model_add_line... INFO @ Tue, 14 Jul 2020 09:46:40: start X-correlation... INFO @ Tue, 14 Jul 2020 09:46:40: end of X-cor INFO @ Tue, 14 Jul 2020 09:46:40: #2 finished! INFO @ Tue, 14 Jul 2020 09:46:40: #2 predicted fragment length is 72 bps INFO @ Tue, 14 Jul 2020 09:46:40: #2 alternative fragment length(s) may be 2,72 bps INFO @ Tue, 14 Jul 2020 09:46:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7351013/SRX7351013.05_model.r WARNING @ Tue, 14 Jul 2020 09:46:40: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:46:40: #2 You may need to consider one of the other alternative d(s): 2,72 WARNING @ Tue, 14 Jul 2020 09:46:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 09:46:40: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:46:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:46:41: 13000000 INFO @ Tue, 14 Jul 2020 09:46:44: 10000000 INFO @ Tue, 14 Jul 2020 09:46:50: 14000000 INFO @ Tue, 14 Jul 2020 09:46:52: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 09:46:59: 15000000 INFO @ Tue, 14 Jul 2020 09:47:00: 12000000 INFO @ Tue, 14 Jul 2020 09:47:07: 16000000 INFO @ Tue, 14 Jul 2020 09:47:08: 13000000 INFO @ Tue, 14 Jul 2020 09:47:16: 17000000 INFO @ Tue, 14 Jul 2020 09:47:16: 14000000 INFO @ Tue, 14 Jul 2020 09:47:17: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:47:24: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 09:47:24: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 09:47:24: #1 total tags in treatment: 17946198 INFO @ Tue, 14 Jul 2020 09:47:24: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:47:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 09:47:24: 15000000 INFO @ Tue, 14 Jul 2020 09:47:24: #1 tags after filtering in treatment: 17946104 INFO @ Tue, 14 Jul 2020 09:47:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:47:24: #1 finished! INFO @ Tue, 14 Jul 2020 09:47:24: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:47:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:47:26: #2 number of paired peaks: 1204 INFO @ Tue, 14 Jul 2020 09:47:26: start model_add_line... INFO @ Tue, 14 Jul 2020 09:47:26: start X-correlation... INFO @ Tue, 14 Jul 2020 09:47:26: end of X-cor INFO @ Tue, 14 Jul 2020 09:47:26: #2 finished! INFO @ Tue, 14 Jul 2020 09:47:26: #2 predicted fragment length is 72 bps INFO @ Tue, 14 Jul 2020 09:47:26: #2 alternative fragment length(s) may be 2,72 bps INFO @ Tue, 14 Jul 2020 09:47:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7351013/SRX7351013.10_model.r WARNING @ Tue, 14 Jul 2020 09:47:26: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:47:26: #2 You may need to consider one of the other alternative d(s): 2,72 WARNING @ Tue, 14 Jul 2020 09:47:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 09:47:26: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:47:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:47:31: 16000000 INFO @ Tue, 14 Jul 2020 09:47:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7351013/SRX7351013.05_peaks.xls INFO @ Tue, 14 Jul 2020 09:47:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7351013/SRX7351013.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:47:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7351013/SRX7351013.05_summits.bed INFO @ Tue, 14 Jul 2020 09:47:34: Done! pass1 - making usageList (604 chroms): 1 millis pass2 - checking and writing primary data (3103 records, 4 fields): 18 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 09:47:38: 17000000 INFO @ Tue, 14 Jul 2020 09:47:45: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 09:47:45: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 09:47:45: #1 total tags in treatment: 17946198 INFO @ Tue, 14 Jul 2020 09:47:45: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:47:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 09:47:45: #1 tags after filtering in treatment: 17946104 INFO @ Tue, 14 Jul 2020 09:47:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:47:45: #1 finished! INFO @ Tue, 14 Jul 2020 09:47:45: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:47:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:47:46: #2 number of paired peaks: 1204 INFO @ Tue, 14 Jul 2020 09:47:46: start model_add_line... INFO @ Tue, 14 Jul 2020 09:47:47: start X-correlation... INFO @ Tue, 14 Jul 2020 09:47:47: end of X-cor INFO @ Tue, 14 Jul 2020 09:47:47: #2 finished! INFO @ Tue, 14 Jul 2020 09:47:47: #2 predicted fragment length is 72 bps INFO @ Tue, 14 Jul 2020 09:47:47: #2 alternative fragment length(s) may be 2,72 bps INFO @ Tue, 14 Jul 2020 09:47:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7351013/SRX7351013.20_model.r WARNING @ Tue, 14 Jul 2020 09:47:47: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:47:47: #2 You may need to consider one of the other alternative d(s): 2,72 WARNING @ Tue, 14 Jul 2020 09:47:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 09:47:47: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:47:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:48:01: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:48:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7351013/SRX7351013.10_peaks.xls INFO @ Tue, 14 Jul 2020 09:48:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7351013/SRX7351013.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:48:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7351013/SRX7351013.10_summits.bed INFO @ Tue, 14 Jul 2020 09:48:18: Done! pass1 - making usageList (538 chroms): 1 millis pass2 - checking and writing primary data (1896 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:48:21: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:48:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7351013/SRX7351013.20_peaks.xls INFO @ Tue, 14 Jul 2020 09:48:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7351013/SRX7351013.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:48:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7351013/SRX7351013.20_summits.bed INFO @ Tue, 14 Jul 2020 09:48:39: Done! pass1 - making usageList (376 chroms): 1 millis pass2 - checking and writing primary data (895 records, 4 fields): 11 millis CompletedMACS2peakCalling