Job ID = 14171930 SRX = SRX9427700 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 19696958 spots for SRR12975507/SRR12975507.sra Written 19696958 spots for SRR12975507/SRR12975507.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172418 ("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: 00:09:08 19696958 reads; of these: 19696958 (100.00%) were unpaired; of these: 7517795 (38.17%) aligned 0 times 3201786 (16.26%) aligned exactly 1 time 8977377 (45.58%) aligned >1 times 61.83% overall alignment rate Time searching: 00:09:08 Overall time: 00:09:08 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 8 files... [bam_rmdupse_core] 4046045 / 12179163 = 0.3322 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 13:39:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9427700/SRX9427700.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9427700/SRX9427700.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9427700/SRX9427700.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9427700/SRX9427700.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 13:39:30: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:39:30: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:39:36: 1000000 INFO @ Sat, 11 Dec 2021 13:39:41: 2000000 INFO @ Sat, 11 Dec 2021 13:39:47: 3000000 INFO @ Sat, 11 Dec 2021 13:39:52: 4000000 INFO @ Sat, 11 Dec 2021 13:39:58: 5000000 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 13:40:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9427700/SRX9427700.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9427700/SRX9427700.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9427700/SRX9427700.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9427700/SRX9427700.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 13:40:00: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:40:00: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:40:03: 6000000 INFO @ Sat, 11 Dec 2021 13:40:07: 1000000 INFO @ Sat, 11 Dec 2021 13:40:09: 7000000 INFO @ Sat, 11 Dec 2021 13:40:14: 2000000 INFO @ Sat, 11 Dec 2021 13:40:14: 8000000 INFO @ Sat, 11 Dec 2021 13:40:15: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:40:15: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:40:15: #1 total tags in treatment: 8133118 INFO @ Sat, 11 Dec 2021 13:40:15: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:40:15: #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 13:40:15: #1 tags after filtering in treatment: 8133118 INFO @ Sat, 11 Dec 2021 13:40:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:40:15: #1 finished! INFO @ Sat, 11 Dec 2021 13:40:15: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:40:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:40:16: #2 number of paired peaks: 5784 INFO @ Sat, 11 Dec 2021 13:40:16: start model_add_line... INFO @ Sat, 11 Dec 2021 13:40:16: start X-correlation... INFO @ Sat, 11 Dec 2021 13:40:16: end of X-cor INFO @ Sat, 11 Dec 2021 13:40:16: #2 finished! INFO @ Sat, 11 Dec 2021 13:40:16: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 13:40:16: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 11 Dec 2021 13:40:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9427700/SRX9427700.05_model.r WARNING @ Sat, 11 Dec 2021 13:40:16: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:40:16: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 11 Dec 2021 13:40:16: #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 13:40:16: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:40:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:40:21: 3000000 INFO @ Sat, 11 Dec 2021 13:40:28: 4000000 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 13:40:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9427700/SRX9427700.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9427700/SRX9427700.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9427700/SRX9427700.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9427700/SRX9427700.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 13:40:30: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:40:30: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:40:33: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:40:34: 5000000 INFO @ Sat, 11 Dec 2021 13:40:36: 1000000 INFO @ Sat, 11 Dec 2021 13:40:41: 6000000 INFO @ Sat, 11 Dec 2021 13:40:42: 2000000 INFO @ Sat, 11 Dec 2021 13:40:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9427700/SRX9427700.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:40:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9427700/SRX9427700.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:40:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9427700/SRX9427700.05_summits.bed INFO @ Sat, 11 Dec 2021 13:40:44: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (12559 records, 4 fields): 45 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:40:47: 3000000 INFO @ Sat, 11 Dec 2021 13:40:48: 7000000 INFO @ Sat, 11 Dec 2021 13:40:53: 4000000 INFO @ Sat, 11 Dec 2021 13:40:54: 8000000 INFO @ Sat, 11 Dec 2021 13:40:55: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:40:55: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:40:55: #1 total tags in treatment: 8133118 INFO @ Sat, 11 Dec 2021 13:40:55: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:40:55: #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 13:40:55: #1 tags after filtering in treatment: 8133118 INFO @ Sat, 11 Dec 2021 13:40:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:40:55: #1 finished! INFO @ Sat, 11 Dec 2021 13:40:55: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:40:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:40:56: #2 number of paired peaks: 5784 INFO @ Sat, 11 Dec 2021 13:40:56: start model_add_line... INFO @ Sat, 11 Dec 2021 13:40:57: start X-correlation... INFO @ Sat, 11 Dec 2021 13:40:57: end of X-cor INFO @ Sat, 11 Dec 2021 13:40:57: #2 finished! INFO @ Sat, 11 Dec 2021 13:40:57: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 13:40:57: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 11 Dec 2021 13:40:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9427700/SRX9427700.10_model.r WARNING @ Sat, 11 Dec 2021 13:40:57: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:40:57: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 11 Dec 2021 13:40:57: #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 13:40:57: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:40:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:40:59: 5000000 INFO @ Sat, 11 Dec 2021 13:41:04: 6000000 INFO @ Sat, 11 Dec 2021 13:41:09: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:41:14: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:41:15: 8000000 INFO @ Sat, 11 Dec 2021 13:41:15: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:41:15: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:41:15: #1 total tags in treatment: 8133118 INFO @ Sat, 11 Dec 2021 13:41:15: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:41:15: #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 13:41:16: #1 tags after filtering in treatment: 8133118 INFO @ Sat, 11 Dec 2021 13:41:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:41:16: #1 finished! INFO @ Sat, 11 Dec 2021 13:41:16: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:41:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:41:17: #2 number of paired peaks: 5784 INFO @ Sat, 11 Dec 2021 13:41:17: start model_add_line... INFO @ Sat, 11 Dec 2021 13:41:17: start X-correlation... INFO @ Sat, 11 Dec 2021 13:41:17: end of X-cor INFO @ Sat, 11 Dec 2021 13:41:17: #2 finished! INFO @ Sat, 11 Dec 2021 13:41:17: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 13:41:17: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 11 Dec 2021 13:41:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9427700/SRX9427700.20_model.r WARNING @ Sat, 11 Dec 2021 13:41:17: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:41:17: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 11 Dec 2021 13:41:17: #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 13:41:17: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:41:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:41:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9427700/SRX9427700.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:41:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9427700/SRX9427700.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:41:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9427700/SRX9427700.10_summits.bed INFO @ Sat, 11 Dec 2021 13:41:25: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6037 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:41:33: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:41:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9427700/SRX9427700.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:41:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9427700/SRX9427700.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:41:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9427700/SRX9427700.20_summits.bed INFO @ Sat, 11 Dec 2021 13:41:43: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1531 records, 4 fields): 4 millis CompletedMACS2peakCalling