Job ID = 6627041 SRX = SRX7351014 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: 00:10:26 26994583 reads; of these: 26994583 (100.00%) were unpaired; of these: 789428 (2.92%) aligned 0 times 17601666 (65.20%) aligned exactly 1 time 8603489 (31.87%) aligned >1 times 97.08% overall alignment rate Time searching: 00:10:26 Overall time: 00:10:26 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] 5578404 / 26205155 = 0.2129 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 09:51:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7351014/SRX7351014.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7351014/SRX7351014.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7351014/SRX7351014.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7351014/SRX7351014.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 09:51:35: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:51:35: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:51:41: 1000000 INFO @ Tue, 14 Jul 2020 09:51:47: 2000000 INFO @ Tue, 14 Jul 2020 09:51:53: 3000000 INFO @ Tue, 14 Jul 2020 09:51:59: 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 09:52:04: 5000000 INFO @ Tue, 14 Jul 2020 09:52:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7351014/SRX7351014.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7351014/SRX7351014.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7351014/SRX7351014.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7351014/SRX7351014.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 09:52:05: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:52:05: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:52:10: 6000000 INFO @ Tue, 14 Jul 2020 09:52:11: 1000000 INFO @ Tue, 14 Jul 2020 09:52:16: 7000000 INFO @ Tue, 14 Jul 2020 09:52:17: 2000000 INFO @ Tue, 14 Jul 2020 09:52:22: 8000000 INFO @ Tue, 14 Jul 2020 09:52:23: 3000000 INFO @ Tue, 14 Jul 2020 09:52:28: 9000000 INFO @ Tue, 14 Jul 2020 09:52:29: 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 09:52:33: 10000000 INFO @ Tue, 14 Jul 2020 09:52:35: 5000000 INFO @ Tue, 14 Jul 2020 09:52:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7351014/SRX7351014.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7351014/SRX7351014.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7351014/SRX7351014.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7351014/SRX7351014.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 09:52:35: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:52:35: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:52:39: 11000000 INFO @ Tue, 14 Jul 2020 09:52:40: 6000000 INFO @ Tue, 14 Jul 2020 09:52:41: 1000000 INFO @ Tue, 14 Jul 2020 09:52:45: 12000000 INFO @ Tue, 14 Jul 2020 09:52:46: 7000000 INFO @ Tue, 14 Jul 2020 09:52:47: 2000000 INFO @ Tue, 14 Jul 2020 09:52:51: 13000000 INFO @ Tue, 14 Jul 2020 09:52:52: 8000000 INFO @ Tue, 14 Jul 2020 09:52:53: 3000000 INFO @ Tue, 14 Jul 2020 09:52:56: 14000000 INFO @ Tue, 14 Jul 2020 09:52:58: 9000000 INFO @ Tue, 14 Jul 2020 09:52:58: 4000000 INFO @ Tue, 14 Jul 2020 09:53:02: 15000000 INFO @ Tue, 14 Jul 2020 09:53:04: 5000000 INFO @ Tue, 14 Jul 2020 09:53:04: 10000000 INFO @ Tue, 14 Jul 2020 09:53:08: 16000000 INFO @ Tue, 14 Jul 2020 09:53:09: 6000000 INFO @ Tue, 14 Jul 2020 09:53:10: 11000000 INFO @ Tue, 14 Jul 2020 09:53:14: 17000000 INFO @ Tue, 14 Jul 2020 09:53:14: 7000000 INFO @ Tue, 14 Jul 2020 09:53:15: 12000000 INFO @ Tue, 14 Jul 2020 09:53:20: 18000000 INFO @ Tue, 14 Jul 2020 09:53:20: 8000000 INFO @ Tue, 14 Jul 2020 09:53:21: 13000000 INFO @ Tue, 14 Jul 2020 09:53:25: 9000000 INFO @ Tue, 14 Jul 2020 09:53:26: 19000000 INFO @ Tue, 14 Jul 2020 09:53:27: 14000000 INFO @ Tue, 14 Jul 2020 09:53:30: 10000000 INFO @ Tue, 14 Jul 2020 09:53:32: 20000000 INFO @ Tue, 14 Jul 2020 09:53:33: 15000000 INFO @ Tue, 14 Jul 2020 09:53:36: 11000000 INFO @ Tue, 14 Jul 2020 09:53:36: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 09:53:36: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 09:53:36: #1 total tags in treatment: 20626751 INFO @ Tue, 14 Jul 2020 09:53:36: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:53:36: #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 09:53:36: #1 tags after filtering in treatment: 20626664 INFO @ Tue, 14 Jul 2020 09:53:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:53:36: #1 finished! INFO @ Tue, 14 Jul 2020 09:53:36: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:53:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:53:38: #2 number of paired peaks: 1050 INFO @ Tue, 14 Jul 2020 09:53:38: start model_add_line... INFO @ Tue, 14 Jul 2020 09:53:38: start X-correlation... INFO @ Tue, 14 Jul 2020 09:53:38: end of X-cor INFO @ Tue, 14 Jul 2020 09:53:38: #2 finished! INFO @ Tue, 14 Jul 2020 09:53:38: #2 predicted fragment length is 72 bps INFO @ Tue, 14 Jul 2020 09:53:38: #2 alternative fragment length(s) may be 2,72 bps INFO @ Tue, 14 Jul 2020 09:53:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7351014/SRX7351014.05_model.r WARNING @ Tue, 14 Jul 2020 09:53:38: #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 09:53:38: #2 You may need to consider one of the other alternative d(s): 2,72 WARNING @ Tue, 14 Jul 2020 09:53:38: #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 09:53:38: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:53:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:53:39: 16000000 INFO @ Tue, 14 Jul 2020 09:53:41: 12000000 INFO @ Tue, 14 Jul 2020 09:53:45: 17000000 INFO @ Tue, 14 Jul 2020 09:53:46: 13000000 INFO @ Tue, 14 Jul 2020 09:53:51: 18000000 INFO @ Tue, 14 Jul 2020 09:53:52: 14000000 INFO @ Tue, 14 Jul 2020 09:53:57: 19000000 INFO @ Tue, 14 Jul 2020 09:53:57: 15000000 INFO @ Tue, 14 Jul 2020 09:54:02: 16000000 INFO @ Tue, 14 Jul 2020 09:54:03: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 09:54:07: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 09:54:07: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 09:54:07: #1 total tags in treatment: 20626751 INFO @ Tue, 14 Jul 2020 09:54:07: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:54:07: #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 09:54:07: #1 tags after filtering in treatment: 20626664 INFO @ Tue, 14 Jul 2020 09:54:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:54:07: #1 finished! INFO @ Tue, 14 Jul 2020 09:54:07: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:54:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:54:08: 17000000 INFO @ Tue, 14 Jul 2020 09:54:09: #2 number of paired peaks: 1050 INFO @ Tue, 14 Jul 2020 09:54:09: start model_add_line... INFO @ Tue, 14 Jul 2020 09:54:09: start X-correlation... INFO @ Tue, 14 Jul 2020 09:54:09: end of X-cor INFO @ Tue, 14 Jul 2020 09:54:09: #2 finished! INFO @ Tue, 14 Jul 2020 09:54:09: #2 predicted fragment length is 72 bps INFO @ Tue, 14 Jul 2020 09:54:09: #2 alternative fragment length(s) may be 2,72 bps INFO @ Tue, 14 Jul 2020 09:54:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7351014/SRX7351014.10_model.r WARNING @ Tue, 14 Jul 2020 09:54:09: #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 09:54:09: #2 You may need to consider one of the other alternative d(s): 2,72 WARNING @ Tue, 14 Jul 2020 09:54:09: #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 09:54:09: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:54:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:54:13: 18000000 INFO @ Tue, 14 Jul 2020 09:54:14: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:54:18: 19000000 INFO @ Tue, 14 Jul 2020 09:54:23: 20000000 INFO @ Tue, 14 Jul 2020 09:54:27: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 09:54:27: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 09:54:27: #1 total tags in treatment: 20626751 INFO @ Tue, 14 Jul 2020 09:54:27: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:54:27: #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 09:54:27: #1 tags after filtering in treatment: 20626664 INFO @ Tue, 14 Jul 2020 09:54:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:54:27: #1 finished! INFO @ Tue, 14 Jul 2020 09:54:27: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:54:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:54:29: #2 number of paired peaks: 1050 INFO @ Tue, 14 Jul 2020 09:54:29: start model_add_line... INFO @ Tue, 14 Jul 2020 09:54:29: start X-correlation... INFO @ Tue, 14 Jul 2020 09:54:29: end of X-cor INFO @ Tue, 14 Jul 2020 09:54:29: #2 finished! INFO @ Tue, 14 Jul 2020 09:54:29: #2 predicted fragment length is 72 bps INFO @ Tue, 14 Jul 2020 09:54:29: #2 alternative fragment length(s) may be 2,72 bps INFO @ Tue, 14 Jul 2020 09:54:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7351014/SRX7351014.20_model.r WARNING @ Tue, 14 Jul 2020 09:54:29: #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 09:54:29: #2 You may need to consider one of the other alternative d(s): 2,72 WARNING @ Tue, 14 Jul 2020 09:54:29: #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 09:54:29: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:54:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:54:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7351014/SRX7351014.05_peaks.xls INFO @ Tue, 14 Jul 2020 09:54:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7351014/SRX7351014.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:54:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7351014/SRX7351014.05_summits.bed INFO @ Tue, 14 Jul 2020 09:54:32: Done! pass1 - making usageList (643 chroms): 2 millis pass2 - checking and writing primary data (3181 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:54:47: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 09:55:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7351014/SRX7351014.10_peaks.xls INFO @ Tue, 14 Jul 2020 09:55:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7351014/SRX7351014.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:55:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7351014/SRX7351014.10_summits.bed INFO @ Tue, 14 Jul 2020 09:55:05: Done! pass1 - making usageList (559 chroms): 1 millis pass2 - checking and writing primary data (1974 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:55:07: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:55:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7351014/SRX7351014.20_peaks.xls INFO @ Tue, 14 Jul 2020 09:55:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7351014/SRX7351014.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:55:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7351014/SRX7351014.20_summits.bed INFO @ Tue, 14 Jul 2020 09:55:24: Done! pass1 - making usageList (392 chroms): 1 millis pass2 - checking and writing primary data (959 records, 4 fields): 12 millis CompletedMACS2peakCalling