Job ID = 6627029 SRX = SRX7351018 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: 00:08:09 24506640 reads; of these: 24506640 (100.00%) were unpaired; of these: 673816 (2.75%) aligned 0 times 19733394 (80.52%) aligned exactly 1 time 4099430 (16.73%) aligned >1 times 97.25% overall alignment rate Time searching: 00:08:09 Overall time: 00:08:09 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] 7423750 / 23832824 = 0.3115 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 09:45:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7351018/SRX7351018.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7351018/SRX7351018.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7351018/SRX7351018.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7351018/SRX7351018.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 09:45:00: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:45:00: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:45:06: 1000000 INFO @ Tue, 14 Jul 2020 09:45:12: 2000000 INFO @ Tue, 14 Jul 2020 09:45:18: 3000000 INFO @ Tue, 14 Jul 2020 09:45:24: 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 09:45:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7351018/SRX7351018.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7351018/SRX7351018.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7351018/SRX7351018.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7351018/SRX7351018.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 09:45:30: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:45:30: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:45:30: 5000000 INFO @ Tue, 14 Jul 2020 09:45:37: 6000000 INFO @ Tue, 14 Jul 2020 09:45:37: 1000000 INFO @ Tue, 14 Jul 2020 09:45:43: 7000000 INFO @ Tue, 14 Jul 2020 09:45:44: 2000000 INFO @ Tue, 14 Jul 2020 09:45:49: 8000000 INFO @ Tue, 14 Jul 2020 09:45:50: 3000000 INFO @ Tue, 14 Jul 2020 09:45:55: 9000000 INFO @ Tue, 14 Jul 2020 09:45:57: 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, 14 Jul 2020 09:46:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7351018/SRX7351018.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7351018/SRX7351018.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7351018/SRX7351018.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7351018/SRX7351018.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 09:46:00: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:46:00: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:46:01: 10000000 INFO @ Tue, 14 Jul 2020 09:46:03: 5000000 INFO @ Tue, 14 Jul 2020 09:46:07: 1000000 INFO @ Tue, 14 Jul 2020 09:46:07: 11000000 INFO @ Tue, 14 Jul 2020 09:46:10: 6000000 INFO @ Tue, 14 Jul 2020 09:46:14: 12000000 INFO @ Tue, 14 Jul 2020 09:46:14: 2000000 INFO @ Tue, 14 Jul 2020 09:46:17: 7000000 INFO @ Tue, 14 Jul 2020 09:46:20: 13000000 INFO @ Tue, 14 Jul 2020 09:46:20: 3000000 INFO @ Tue, 14 Jul 2020 09:46:23: 8000000 INFO @ Tue, 14 Jul 2020 09:46:26: 14000000 INFO @ Tue, 14 Jul 2020 09:46:27: 4000000 INFO @ Tue, 14 Jul 2020 09:46:30: 9000000 INFO @ Tue, 14 Jul 2020 09:46:33: 15000000 INFO @ Tue, 14 Jul 2020 09:46:33: 5000000 INFO @ Tue, 14 Jul 2020 09:46:37: 10000000 INFO @ Tue, 14 Jul 2020 09:46:39: 16000000 INFO @ Tue, 14 Jul 2020 09:46:40: 6000000 INFO @ Tue, 14 Jul 2020 09:46:42: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 09:46:42: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 09:46:42: #1 total tags in treatment: 16409074 INFO @ Tue, 14 Jul 2020 09:46:42: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:46:42: #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 09:46:42: #1 tags after filtering in treatment: 16408841 INFO @ Tue, 14 Jul 2020 09:46:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:46:42: #1 finished! INFO @ Tue, 14 Jul 2020 09:46:42: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:46:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:46:43: 11000000 INFO @ Tue, 14 Jul 2020 09:46:45: #2 number of paired peaks: 11450 INFO @ Tue, 14 Jul 2020 09:46:45: start model_add_line... INFO @ Tue, 14 Jul 2020 09:46:45: start X-correlation... INFO @ Tue, 14 Jul 2020 09:46:45: end of X-cor INFO @ Tue, 14 Jul 2020 09:46:45: #2 finished! INFO @ Tue, 14 Jul 2020 09:46:45: #2 predicted fragment length is 148 bps INFO @ Tue, 14 Jul 2020 09:46:45: #2 alternative fragment length(s) may be 148 bps INFO @ Tue, 14 Jul 2020 09:46:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7351018/SRX7351018.05_model.r WARNING @ Tue, 14 Jul 2020 09:46:45: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:46:45: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Tue, 14 Jul 2020 09:46:45: #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 09:46:45: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:46:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:46:47: 7000000 INFO @ Tue, 14 Jul 2020 09:46:50: 12000000 INFO @ Tue, 14 Jul 2020 09:46:53: 8000000 INFO @ Tue, 14 Jul 2020 09:46:56: 13000000 INFO @ Tue, 14 Jul 2020 09:46:59: 9000000 INFO @ Tue, 14 Jul 2020 09:47:03: 14000000 INFO @ Tue, 14 Jul 2020 09:47:05: 10000000 INFO @ Tue, 14 Jul 2020 09:47:10: 15000000 INFO @ Tue, 14 Jul 2020 09:47:11: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 09:47:16: 16000000 INFO @ Tue, 14 Jul 2020 09:47:18: 12000000 INFO @ Tue, 14 Jul 2020 09:47:19: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 09:47:19: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 09:47:19: #1 total tags in treatment: 16409074 INFO @ Tue, 14 Jul 2020 09:47:19: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:47:19: #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 09:47:19: #1 tags after filtering in treatment: 16408841 INFO @ Tue, 14 Jul 2020 09:47:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:47:19: #1 finished! INFO @ Tue, 14 Jul 2020 09:47:19: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:47:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:47:22: #2 number of paired peaks: 11450 INFO @ Tue, 14 Jul 2020 09:47:22: start model_add_line... INFO @ Tue, 14 Jul 2020 09:47:22: start X-correlation... INFO @ Tue, 14 Jul 2020 09:47:22: end of X-cor INFO @ Tue, 14 Jul 2020 09:47:22: #2 finished! INFO @ Tue, 14 Jul 2020 09:47:22: #2 predicted fragment length is 148 bps INFO @ Tue, 14 Jul 2020 09:47:22: #2 alternative fragment length(s) may be 148 bps INFO @ Tue, 14 Jul 2020 09:47:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7351018/SRX7351018.10_model.r WARNING @ Tue, 14 Jul 2020 09:47:22: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:47:22: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Tue, 14 Jul 2020 09:47:22: #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 09:47:22: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:47:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:47:24: 13000000 INFO @ Tue, 14 Jul 2020 09:47:30: 14000000 INFO @ Tue, 14 Jul 2020 09:47:36: 15000000 INFO @ Tue, 14 Jul 2020 09:47:38: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 09:47:42: 16000000 INFO @ Tue, 14 Jul 2020 09:47:44: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 09:47:44: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 09:47:44: #1 total tags in treatment: 16409074 INFO @ Tue, 14 Jul 2020 09:47:44: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:47:44: #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: 16408841 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 09:47:47: #2 number of paired peaks: 11450 INFO @ Tue, 14 Jul 2020 09:47:47: start model_add_line... INFO @ Tue, 14 Jul 2020 09:47:48: start X-correlation... INFO @ Tue, 14 Jul 2020 09:47:48: end of X-cor INFO @ Tue, 14 Jul 2020 09:47:48: #2 finished! INFO @ Tue, 14 Jul 2020 09:47:48: #2 predicted fragment length is 148 bps INFO @ Tue, 14 Jul 2020 09:47:48: #2 alternative fragment length(s) may be 148 bps INFO @ Tue, 14 Jul 2020 09:47:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7351018/SRX7351018.20_model.r WARNING @ Tue, 14 Jul 2020 09:47:48: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:47:48: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Tue, 14 Jul 2020 09:47:48: #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 09:47:48: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:47:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:48:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7351018/SRX7351018.05_peaks.xls INFO @ Tue, 14 Jul 2020 09:48:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7351018/SRX7351018.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:48:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7351018/SRX7351018.05_summits.bed INFO @ Tue, 14 Jul 2020 09:48:01: Done! pass1 - making usageList (195 chroms): 3 millis pass2 - checking and writing primary data (13682 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:48:14: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:48:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7351018/SRX7351018.10_peaks.xls INFO @ Tue, 14 Jul 2020 09:48:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7351018/SRX7351018.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:48:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7351018/SRX7351018.10_summits.bed INFO @ Tue, 14 Jul 2020 09:48:36: Done! pass1 - making usageList (174 chroms): 3 millis pass2 - checking and writing primary data (11358 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:48:40: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:49:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7351018/SRX7351018.20_peaks.xls INFO @ Tue, 14 Jul 2020 09:49:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7351018/SRX7351018.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:49:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7351018/SRX7351018.20_summits.bed INFO @ Tue, 14 Jul 2020 09:49:02: Done! pass1 - making usageList (138 chroms): 2 millis pass2 - checking and writing primary data (8040 records, 4 fields): 14 millis CompletedMACS2peakCalling