Job ID = 14170657 SRX = SRX9434473 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 28824921 spots for SRR12982871/SRR12982871.sra Written 28824921 spots for SRR12982871/SRR12982871.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171135 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:17:27 28824921 reads; of these: 28824921 (100.00%) were unpaired; of these: 441789 (1.53%) aligned 0 times 6479010 (22.48%) aligned exactly 1 time 21904122 (75.99%) aligned >1 times 98.47% overall alignment rate Time searching: 00:17:27 Overall time: 00:17:27 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 11289503 / 28383132 = 0.3978 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 08:16:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9434473/SRX9434473.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9434473/SRX9434473.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9434473/SRX9434473.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9434473/SRX9434473.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 @ Sat, 11 Dec 2021 08:16:51: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:16:51: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:17:00: 1000000 INFO @ Sat, 11 Dec 2021 08:17:09: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 08:17:18: 3000000 INFO @ Sat, 11 Dec 2021 08:17:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9434473/SRX9434473.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9434473/SRX9434473.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9434473/SRX9434473.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9434473/SRX9434473.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 @ Sat, 11 Dec 2021 08:17:21: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:17:21: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:17:27: 4000000 INFO @ Sat, 11 Dec 2021 08:17:30: 1000000 INFO @ Sat, 11 Dec 2021 08:17:37: 5000000 INFO @ Sat, 11 Dec 2021 08:17:40: 2000000 INFO @ Sat, 11 Dec 2021 08:17:46: 6000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 08:17:50: 3000000 INFO @ Sat, 11 Dec 2021 08:17:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9434473/SRX9434473.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9434473/SRX9434473.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9434473/SRX9434473.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9434473/SRX9434473.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 @ Sat, 11 Dec 2021 08:17:51: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:17:51: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:17:55: 7000000 INFO @ Sat, 11 Dec 2021 08:17:59: 4000000 INFO @ Sat, 11 Dec 2021 08:17:59: 1000000 INFO @ Sat, 11 Dec 2021 08:18:05: 8000000 INFO @ Sat, 11 Dec 2021 08:18:08: 2000000 INFO @ Sat, 11 Dec 2021 08:18:08: 5000000 INFO @ Sat, 11 Dec 2021 08:18:14: 9000000 INFO @ Sat, 11 Dec 2021 08:18:16: 3000000 INFO @ Sat, 11 Dec 2021 08:18:18: 6000000 INFO @ Sat, 11 Dec 2021 08:18:23: 10000000 INFO @ Sat, 11 Dec 2021 08:18:25: 4000000 INFO @ Sat, 11 Dec 2021 08:18:28: 7000000 INFO @ Sat, 11 Dec 2021 08:18:32: 11000000 INFO @ Sat, 11 Dec 2021 08:18:33: 5000000 INFO @ Sat, 11 Dec 2021 08:18:37: 8000000 INFO @ Sat, 11 Dec 2021 08:18:41: 6000000 INFO @ Sat, 11 Dec 2021 08:18:42: 12000000 INFO @ Sat, 11 Dec 2021 08:18:47: 9000000 INFO @ Sat, 11 Dec 2021 08:18:49: 7000000 INFO @ Sat, 11 Dec 2021 08:18:51: 13000000 INFO @ Sat, 11 Dec 2021 08:18:57: 10000000 INFO @ Sat, 11 Dec 2021 08:18:58: 8000000 INFO @ Sat, 11 Dec 2021 08:19:00: 14000000 INFO @ Sat, 11 Dec 2021 08:19:06: 9000000 INFO @ Sat, 11 Dec 2021 08:19:06: 11000000 INFO @ Sat, 11 Dec 2021 08:19:10: 15000000 INFO @ Sat, 11 Dec 2021 08:19:15: 10000000 INFO @ Sat, 11 Dec 2021 08:19:16: 12000000 INFO @ Sat, 11 Dec 2021 08:19:19: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 08:19:23: 11000000 INFO @ Sat, 11 Dec 2021 08:19:26: 13000000 INFO @ Sat, 11 Dec 2021 08:19:29: 17000000 INFO @ Sat, 11 Dec 2021 08:19:30: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:19:30: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:19:30: #1 total tags in treatment: 17093629 INFO @ Sat, 11 Dec 2021 08:19:30: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:19:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 08:19:30: #1 tags after filtering in treatment: 17093629 INFO @ Sat, 11 Dec 2021 08:19:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:19:30: #1 finished! INFO @ Sat, 11 Dec 2021 08:19:30: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:19:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:19:32: 12000000 INFO @ Sat, 11 Dec 2021 08:19:32: #2 number of paired peaks: 5362 INFO @ Sat, 11 Dec 2021 08:19:32: start model_add_line... INFO @ Sat, 11 Dec 2021 08:19:33: start X-correlation... INFO @ Sat, 11 Dec 2021 08:19:33: end of X-cor INFO @ Sat, 11 Dec 2021 08:19:33: #2 finished! INFO @ Sat, 11 Dec 2021 08:19:33: #2 predicted fragment length is 61 bps INFO @ Sat, 11 Dec 2021 08:19:33: #2 alternative fragment length(s) may be 4,61 bps INFO @ Sat, 11 Dec 2021 08:19:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9434473/SRX9434473.05_model.r WARNING @ Sat, 11 Dec 2021 08:19:33: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:19:33: #2 You may need to consider one of the other alternative d(s): 4,61 WARNING @ Sat, 11 Dec 2021 08:19:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 08:19:33: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:19:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:19:36: 14000000 INFO @ Sat, 11 Dec 2021 08:19:40: 13000000 INFO @ Sat, 11 Dec 2021 08:19:45: 15000000 INFO @ Sat, 11 Dec 2021 08:19:49: 14000000 INFO @ Sat, 11 Dec 2021 08:19:55: 16000000 INFO @ Sat, 11 Dec 2021 08:19:57: 15000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 08:20:04: 17000000 INFO @ Sat, 11 Dec 2021 08:20:05: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:20:05: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:20:05: #1 total tags in treatment: 17093629 INFO @ Sat, 11 Dec 2021 08:20:05: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:20:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 08:20:05: 16000000 INFO @ Sat, 11 Dec 2021 08:20:05: #1 tags after filtering in treatment: 17093629 INFO @ Sat, 11 Dec 2021 08:20:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:20:05: #1 finished! INFO @ Sat, 11 Dec 2021 08:20:05: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:20:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:20:08: #2 number of paired peaks: 5362 INFO @ Sat, 11 Dec 2021 08:20:08: start model_add_line... INFO @ Sat, 11 Dec 2021 08:20:08: start X-correlation... INFO @ Sat, 11 Dec 2021 08:20:08: end of X-cor INFO @ Sat, 11 Dec 2021 08:20:08: #2 finished! INFO @ Sat, 11 Dec 2021 08:20:08: #2 predicted fragment length is 61 bps INFO @ Sat, 11 Dec 2021 08:20:08: #2 alternative fragment length(s) may be 4,61 bps INFO @ Sat, 11 Dec 2021 08:20:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9434473/SRX9434473.10_model.r WARNING @ Sat, 11 Dec 2021 08:20:08: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:20:08: #2 You may need to consider one of the other alternative d(s): 4,61 WARNING @ Sat, 11 Dec 2021 08:20:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 08:20:08: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:20:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:20:13: 17000000 INFO @ Sat, 11 Dec 2021 08:20:14: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:20:14: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:20:14: #1 total tags in treatment: 17093629 INFO @ Sat, 11 Dec 2021 08:20:14: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:20:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 08:20:14: #1 tags after filtering in treatment: 17093629 INFO @ Sat, 11 Dec 2021 08:20:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:20:14: #1 finished! INFO @ Sat, 11 Dec 2021 08:20:14: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:20:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:20:17: #2 number of paired peaks: 5362 INFO @ Sat, 11 Dec 2021 08:20:17: start model_add_line... INFO @ Sat, 11 Dec 2021 08:20:17: start X-correlation... INFO @ Sat, 11 Dec 2021 08:20:17: end of X-cor INFO @ Sat, 11 Dec 2021 08:20:17: #2 finished! INFO @ Sat, 11 Dec 2021 08:20:17: #2 predicted fragment length is 61 bps INFO @ Sat, 11 Dec 2021 08:20:17: #2 alternative fragment length(s) may be 4,61 bps INFO @ Sat, 11 Dec 2021 08:20:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9434473/SRX9434473.20_model.r WARNING @ Sat, 11 Dec 2021 08:20:17: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:20:17: #2 You may need to consider one of the other alternative d(s): 4,61 WARNING @ Sat, 11 Dec 2021 08:20:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 08:20:17: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:20:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:20:17: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:20:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9434473/SRX9434473.05_peaks.xls INFO @ Sat, 11 Dec 2021 08:20:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9434473/SRX9434473.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:20:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9434473/SRX9434473.05_summits.bed INFO @ Sat, 11 Dec 2021 08:20:40: Done! pass1 - making usageList (14 chroms): 6 millis pass2 - checking and writing primary data (20896 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:20:53: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:21:01: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:21:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9434473/SRX9434473.10_peaks.xls INFO @ Sat, 11 Dec 2021 08:21:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9434473/SRX9434473.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:21:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9434473/SRX9434473.10_summits.bed INFO @ Sat, 11 Dec 2021 08:21:17: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (11654 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:21:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9434473/SRX9434473.20_peaks.xls INFO @ Sat, 11 Dec 2021 08:21:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9434473/SRX9434473.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:21:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9434473/SRX9434473.20_summits.bed INFO @ Sat, 11 Dec 2021 08:21:24: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (3586 records, 4 fields): 6 millis CompletedMACS2peakCalling