Job ID = 6529415 SRX = SRX2592421 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: 00:10:35 26242199 reads; of these: 26242199 (100.00%) were unpaired; of these: 1987066 (7.57%) aligned 0 times 17948153 (68.39%) aligned exactly 1 time 6306980 (24.03%) aligned >1 times 92.43% overall alignment rate Time searching: 00:10:35 Overall time: 00:10:35 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] 4761526 / 24255133 = 0.1963 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, 30 Jun 2020 02:16:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592421/SRX2592421.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592421/SRX2592421.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592421/SRX2592421.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592421/SRX2592421.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, 30 Jun 2020 02:16:33: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:16:33: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:16:39: 1000000 INFO @ Tue, 30 Jun 2020 02:16:45: 2000000 INFO @ Tue, 30 Jun 2020 02:16:51: 3000000 INFO @ Tue, 30 Jun 2020 02:16:56: 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, 30 Jun 2020 02:17:02: 5000000 INFO @ Tue, 30 Jun 2020 02:17:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592421/SRX2592421.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592421/SRX2592421.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592421/SRX2592421.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592421/SRX2592421.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, 30 Jun 2020 02:17:03: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:17:03: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:17:08: 6000000 INFO @ Tue, 30 Jun 2020 02:17:10: 1000000 INFO @ Tue, 30 Jun 2020 02:17:14: 7000000 INFO @ Tue, 30 Jun 2020 02:17:16: 2000000 INFO @ Tue, 30 Jun 2020 02:17:20: 8000000 INFO @ Tue, 30 Jun 2020 02:17:22: 3000000 INFO @ Tue, 30 Jun 2020 02:17:26: 9000000 INFO @ Tue, 30 Jun 2020 02:17:28: 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, 30 Jun 2020 02:17:32: 10000000 INFO @ Tue, 30 Jun 2020 02:17:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592421/SRX2592421.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592421/SRX2592421.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592421/SRX2592421.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592421/SRX2592421.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, 30 Jun 2020 02:17:34: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:17:34: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:17:34: 5000000 INFO @ Tue, 30 Jun 2020 02:17:38: 11000000 INFO @ Tue, 30 Jun 2020 02:17:40: 1000000 INFO @ Tue, 30 Jun 2020 02:17:40: 6000000 INFO @ Tue, 30 Jun 2020 02:17:45: 12000000 INFO @ Tue, 30 Jun 2020 02:17:46: 7000000 INFO @ Tue, 30 Jun 2020 02:17:47: 2000000 INFO @ Tue, 30 Jun 2020 02:17:51: 13000000 INFO @ Tue, 30 Jun 2020 02:17:52: 8000000 INFO @ Tue, 30 Jun 2020 02:17:53: 3000000 INFO @ Tue, 30 Jun 2020 02:17:58: 14000000 INFO @ Tue, 30 Jun 2020 02:17:59: 9000000 INFO @ Tue, 30 Jun 2020 02:18:00: 4000000 INFO @ Tue, 30 Jun 2020 02:18:04: 15000000 INFO @ Tue, 30 Jun 2020 02:18:05: 10000000 INFO @ Tue, 30 Jun 2020 02:18:07: 5000000 INFO @ Tue, 30 Jun 2020 02:18:11: 11000000 INFO @ Tue, 30 Jun 2020 02:18:12: 16000000 INFO @ Tue, 30 Jun 2020 02:18:14: 6000000 INFO @ Tue, 30 Jun 2020 02:18:17: 12000000 INFO @ Tue, 30 Jun 2020 02:18:19: 17000000 INFO @ Tue, 30 Jun 2020 02:18:20: 7000000 INFO @ Tue, 30 Jun 2020 02:18:23: 13000000 INFO @ Tue, 30 Jun 2020 02:18:26: 18000000 INFO @ Tue, 30 Jun 2020 02:18:27: 8000000 INFO @ Tue, 30 Jun 2020 02:18:29: 14000000 INFO @ Tue, 30 Jun 2020 02:18:34: 19000000 INFO @ Tue, 30 Jun 2020 02:18:34: 9000000 INFO @ Tue, 30 Jun 2020 02:18:35: 15000000 INFO @ Tue, 30 Jun 2020 02:18:38: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:18:38: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:18:38: #1 total tags in treatment: 19493607 INFO @ Tue, 30 Jun 2020 02:18:38: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:18:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:18:39: #1 tags after filtering in treatment: 19493536 INFO @ Tue, 30 Jun 2020 02:18:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:18:39: #1 finished! INFO @ Tue, 30 Jun 2020 02:18:39: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:18:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:18:40: #2 number of paired peaks: 216 WARNING @ Tue, 30 Jun 2020 02:18:40: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Tue, 30 Jun 2020 02:18:40: start model_add_line... INFO @ Tue, 30 Jun 2020 02:18:40: start X-correlation... INFO @ Tue, 30 Jun 2020 02:18:40: end of X-cor INFO @ Tue, 30 Jun 2020 02:18:40: #2 finished! INFO @ Tue, 30 Jun 2020 02:18:40: #2 predicted fragment length is 53 bps INFO @ Tue, 30 Jun 2020 02:18:40: #2 alternative fragment length(s) may be 4,53,549 bps INFO @ Tue, 30 Jun 2020 02:18:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592421/SRX2592421.05_model.r WARNING @ Tue, 30 Jun 2020 02:18:40: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:18:40: #2 You may need to consider one of the other alternative d(s): 4,53,549 WARNING @ Tue, 30 Jun 2020 02:18:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:18:40: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:18:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:18:41: 10000000 INFO @ Tue, 30 Jun 2020 02:18:42: 16000000 INFO @ Tue, 30 Jun 2020 02:18:48: 11000000 INFO @ Tue, 30 Jun 2020 02:18:49: 17000000 INFO @ Tue, 30 Jun 2020 02:18:54: 12000000 INFO @ Tue, 30 Jun 2020 02:18:55: 18000000 INFO @ Tue, 30 Jun 2020 02:19:01: 13000000 INFO @ Tue, 30 Jun 2020 02:19:02: 19000000 INFO @ Tue, 30 Jun 2020 02:19:06: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:19:06: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:19:06: #1 total tags in treatment: 19493607 INFO @ Tue, 30 Jun 2020 02:19:06: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:19:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:19:07: #1 tags after filtering in treatment: 19493536 INFO @ Tue, 30 Jun 2020 02:19:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:19:07: #1 finished! INFO @ Tue, 30 Jun 2020 02:19:07: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:19:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:19:08: 14000000 INFO @ Tue, 30 Jun 2020 02:19:08: #2 number of paired peaks: 216 WARNING @ Tue, 30 Jun 2020 02:19:08: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Tue, 30 Jun 2020 02:19:08: start model_add_line... INFO @ Tue, 30 Jun 2020 02:19:08: start X-correlation... INFO @ Tue, 30 Jun 2020 02:19:08: end of X-cor INFO @ Tue, 30 Jun 2020 02:19:08: #2 finished! INFO @ Tue, 30 Jun 2020 02:19:08: #2 predicted fragment length is 53 bps INFO @ Tue, 30 Jun 2020 02:19:08: #2 alternative fragment length(s) may be 4,53,549 bps INFO @ Tue, 30 Jun 2020 02:19:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592421/SRX2592421.10_model.r WARNING @ Tue, 30 Jun 2020 02:19:08: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:19:08: #2 You may need to consider one of the other alternative d(s): 4,53,549 WARNING @ Tue, 30 Jun 2020 02:19:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:19:08: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:19:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:19:15: 15000000 INFO @ Tue, 30 Jun 2020 02:19:15: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:19:23: 16000000 INFO @ Tue, 30 Jun 2020 02:19:30: 17000000 INFO @ Tue, 30 Jun 2020 02:19:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592421/SRX2592421.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:19:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592421/SRX2592421.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:19:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592421/SRX2592421.05_summits.bed INFO @ Tue, 30 Jun 2020 02:19:35: Done! pass1 - making usageList (738 chroms): 3 millis pass2 - checking and writing primary data (10534 records, 4 fields): 52 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:19:37: 18000000 INFO @ Tue, 30 Jun 2020 02:19:43: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:19:45: 19000000 INFO @ Tue, 30 Jun 2020 02:19:49: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:19:49: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:19:49: #1 total tags in treatment: 19493607 INFO @ Tue, 30 Jun 2020 02:19:49: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:19:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:19:50: #1 tags after filtering in treatment: 19493536 INFO @ Tue, 30 Jun 2020 02:19:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:19:50: #1 finished! INFO @ Tue, 30 Jun 2020 02:19:50: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:19:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:19:51: #2 number of paired peaks: 216 WARNING @ Tue, 30 Jun 2020 02:19:51: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Tue, 30 Jun 2020 02:19:51: start model_add_line... INFO @ Tue, 30 Jun 2020 02:19:51: start X-correlation... INFO @ Tue, 30 Jun 2020 02:19:51: end of X-cor INFO @ Tue, 30 Jun 2020 02:19:51: #2 finished! INFO @ Tue, 30 Jun 2020 02:19:51: #2 predicted fragment length is 53 bps INFO @ Tue, 30 Jun 2020 02:19:51: #2 alternative fragment length(s) may be 4,53,549 bps INFO @ Tue, 30 Jun 2020 02:19:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592421/SRX2592421.20_model.r WARNING @ Tue, 30 Jun 2020 02:19:51: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:19:51: #2 You may need to consider one of the other alternative d(s): 4,53,549 WARNING @ Tue, 30 Jun 2020 02:19:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:19:51: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:19:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:20:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592421/SRX2592421.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:20:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592421/SRX2592421.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:20:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592421/SRX2592421.10_summits.bed INFO @ Tue, 30 Jun 2020 02:20:02: Done! pass1 - making usageList (550 chroms): 2 millis pass2 - checking and writing primary data (4434 records, 4 fields): 34 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:20:26: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:20:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592421/SRX2592421.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:20:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592421/SRX2592421.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:20:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592421/SRX2592421.20_summits.bed INFO @ Tue, 30 Jun 2020 02:20:45: Done! pass1 - making usageList (266 chroms): 2 millis pass2 - checking and writing primary data (694 records, 4 fields): 16 millis CompletedMACS2peakCalling