Job ID = 6627027 SRX = SRX7351016 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: 00:07:04 21401472 reads; of these: 21401472 (100.00%) were unpaired; of these: 643230 (3.01%) aligned 0 times 17218407 (80.45%) aligned exactly 1 time 3539835 (16.54%) aligned >1 times 96.99% overall alignment rate Time searching: 00:07:04 Overall time: 00:07:04 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] 3752603 / 20758242 = 0.1808 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 09:42:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7351016/SRX7351016.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7351016/SRX7351016.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7351016/SRX7351016.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7351016/SRX7351016.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 09:42:06: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:42:06: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:42:12: 1000000 INFO @ Tue, 14 Jul 2020 09:42:17: 2000000 INFO @ Tue, 14 Jul 2020 09:42:23: 3000000 INFO @ Tue, 14 Jul 2020 09:42:28: 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 09:42:34: 5000000 INFO @ Tue, 14 Jul 2020 09:42:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7351016/SRX7351016.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7351016/SRX7351016.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7351016/SRX7351016.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7351016/SRX7351016.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 09:42:36: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:42:36: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:42:41: 6000000 INFO @ Tue, 14 Jul 2020 09:42:44: 1000000 INFO @ Tue, 14 Jul 2020 09:42:47: 7000000 INFO @ Tue, 14 Jul 2020 09:42:51: 2000000 INFO @ Tue, 14 Jul 2020 09:42:54: 8000000 INFO @ Tue, 14 Jul 2020 09:42:59: 3000000 INFO @ Tue, 14 Jul 2020 09:43:00: 9000000 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 09:43:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7351016/SRX7351016.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7351016/SRX7351016.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7351016/SRX7351016.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7351016/SRX7351016.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 09:43:06: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:43:06: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:43:06: 4000000 INFO @ Tue, 14 Jul 2020 09:43:07: 10000000 INFO @ Tue, 14 Jul 2020 09:43:13: 1000000 INFO @ Tue, 14 Jul 2020 09:43:14: 11000000 INFO @ Tue, 14 Jul 2020 09:43:14: 5000000 INFO @ Tue, 14 Jul 2020 09:43:20: 2000000 INFO @ Tue, 14 Jul 2020 09:43:21: 12000000 INFO @ Tue, 14 Jul 2020 09:43:22: 6000000 INFO @ Tue, 14 Jul 2020 09:43:27: 3000000 INFO @ Tue, 14 Jul 2020 09:43:27: 13000000 INFO @ Tue, 14 Jul 2020 09:43:30: 7000000 INFO @ Tue, 14 Jul 2020 09:43:34: 4000000 INFO @ Tue, 14 Jul 2020 09:43:34: 14000000 INFO @ Tue, 14 Jul 2020 09:43:37: 8000000 INFO @ Tue, 14 Jul 2020 09:43:41: 5000000 INFO @ Tue, 14 Jul 2020 09:43:42: 15000000 INFO @ Tue, 14 Jul 2020 09:43:45: 9000000 INFO @ Tue, 14 Jul 2020 09:43:48: 6000000 INFO @ Tue, 14 Jul 2020 09:43:49: 16000000 INFO @ Tue, 14 Jul 2020 09:43:53: 10000000 INFO @ Tue, 14 Jul 2020 09:43:55: 7000000 INFO @ Tue, 14 Jul 2020 09:43:56: 17000000 INFO @ Tue, 14 Jul 2020 09:43:56: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 09:43:56: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 09:43:56: #1 total tags in treatment: 17005639 INFO @ Tue, 14 Jul 2020 09:43:56: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:43:56: #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 09:43:56: #1 tags after filtering in treatment: 17005407 INFO @ Tue, 14 Jul 2020 09:43:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:43:56: #1 finished! INFO @ Tue, 14 Jul 2020 09:43:56: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:43:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:43:58: #2 number of paired peaks: 2998 INFO @ Tue, 14 Jul 2020 09:43:58: start model_add_line... INFO @ Tue, 14 Jul 2020 09:43:58: start X-correlation... INFO @ Tue, 14 Jul 2020 09:43:58: end of X-cor INFO @ Tue, 14 Jul 2020 09:43:58: #2 finished! INFO @ Tue, 14 Jul 2020 09:43:58: #2 predicted fragment length is 135 bps INFO @ Tue, 14 Jul 2020 09:43:58: #2 alternative fragment length(s) may be 4,135 bps INFO @ Tue, 14 Jul 2020 09:43:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7351016/SRX7351016.05_model.r WARNING @ Tue, 14 Jul 2020 09:43:58: #2 Since the d (135) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:43:58: #2 You may need to consider one of the other alternative d(s): 4,135 WARNING @ Tue, 14 Jul 2020 09:43:58: #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 09:43:58: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:43:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:44:01: 11000000 INFO @ Tue, 14 Jul 2020 09:44:04: 8000000 INFO @ Tue, 14 Jul 2020 09:44:09: 12000000 INFO @ Tue, 14 Jul 2020 09:44:10: 9000000 INFO @ Tue, 14 Jul 2020 09:44:17: 13000000 INFO @ Tue, 14 Jul 2020 09:44:17: 10000000 INFO @ Tue, 14 Jul 2020 09:44:24: 11000000 INFO @ Tue, 14 Jul 2020 09:44:25: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 09:44:31: 12000000 INFO @ Tue, 14 Jul 2020 09:44:33: 15000000 INFO @ Tue, 14 Jul 2020 09:44:37: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:44:37: 13000000 INFO @ Tue, 14 Jul 2020 09:44:41: 16000000 INFO @ Tue, 14 Jul 2020 09:44:44: 14000000 INFO @ Tue, 14 Jul 2020 09:44:49: 17000000 INFO @ Tue, 14 Jul 2020 09:44:49: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 09:44:49: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 09:44:49: #1 total tags in treatment: 17005639 INFO @ Tue, 14 Jul 2020 09:44:49: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:44:49: #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 09:44:50: #1 tags after filtering in treatment: 17005407 INFO @ Tue, 14 Jul 2020 09:44:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:44:50: #1 finished! INFO @ Tue, 14 Jul 2020 09:44:50: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:44:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:44:51: 15000000 INFO @ Tue, 14 Jul 2020 09:44:51: #2 number of paired peaks: 2998 INFO @ Tue, 14 Jul 2020 09:44:51: start model_add_line... INFO @ Tue, 14 Jul 2020 09:44:52: start X-correlation... INFO @ Tue, 14 Jul 2020 09:44:52: end of X-cor INFO @ Tue, 14 Jul 2020 09:44:52: #2 finished! INFO @ Tue, 14 Jul 2020 09:44:52: #2 predicted fragment length is 135 bps INFO @ Tue, 14 Jul 2020 09:44:52: #2 alternative fragment length(s) may be 4,135 bps INFO @ Tue, 14 Jul 2020 09:44:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7351016/SRX7351016.10_model.r WARNING @ Tue, 14 Jul 2020 09:44:52: #2 Since the d (135) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:44:52: #2 You may need to consider one of the other alternative d(s): 4,135 WARNING @ Tue, 14 Jul 2020 09:44:52: #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 09:44:52: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:44:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:44:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7351016/SRX7351016.05_peaks.xls INFO @ Tue, 14 Jul 2020 09:44:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7351016/SRX7351016.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:44:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7351016/SRX7351016.05_summits.bed INFO @ Tue, 14 Jul 2020 09:44:55: Done! pass1 - making usageList (202 chroms): 2 millis pass2 - checking and writing primary data (13425 records, 4 fields): 19 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 09:44:57: 16000000 INFO @ Tue, 14 Jul 2020 09:45:04: 17000000 INFO @ Tue, 14 Jul 2020 09:45:04: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 09:45:04: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 09:45:04: #1 total tags in treatment: 17005639 INFO @ Tue, 14 Jul 2020 09:45:04: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:45:04: #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 09:45:04: #1 tags after filtering in treatment: 17005407 INFO @ Tue, 14 Jul 2020 09:45:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:45:04: #1 finished! INFO @ Tue, 14 Jul 2020 09:45:04: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:45:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:45:06: #2 number of paired peaks: 2998 INFO @ Tue, 14 Jul 2020 09:45:06: start model_add_line... INFO @ Tue, 14 Jul 2020 09:45:06: start X-correlation... INFO @ Tue, 14 Jul 2020 09:45:06: end of X-cor INFO @ Tue, 14 Jul 2020 09:45:06: #2 finished! INFO @ Tue, 14 Jul 2020 09:45:06: #2 predicted fragment length is 135 bps INFO @ Tue, 14 Jul 2020 09:45:06: #2 alternative fragment length(s) may be 4,135 bps INFO @ Tue, 14 Jul 2020 09:45:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7351016/SRX7351016.20_model.r WARNING @ Tue, 14 Jul 2020 09:45:06: #2 Since the d (135) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:45:06: #2 You may need to consider one of the other alternative d(s): 4,135 WARNING @ Tue, 14 Jul 2020 09:45:06: #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 09:45:06: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:45:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:45:31: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:45:45: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:45:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7351016/SRX7351016.10_peaks.xls INFO @ Tue, 14 Jul 2020 09:45:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7351016/SRX7351016.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:45:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7351016/SRX7351016.10_summits.bed INFO @ Tue, 14 Jul 2020 09:45:51: Done! pass1 - making usageList (174 chroms): 2 millis pass2 - checking and writing primary data (8930 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:46:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7351016/SRX7351016.20_peaks.xls INFO @ Tue, 14 Jul 2020 09:46:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7351016/SRX7351016.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:46:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7351016/SRX7351016.20_summits.bed INFO @ Tue, 14 Jul 2020 09:46:03: Done! pass1 - making usageList (146 chroms): 2 millis pass2 - checking and writing primary data (4884 records, 4 fields): 9 millis CompletedMACS2peakCalling