Job ID = 14172197 SRX = SRX9427697 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 11017272 spots for SRR12975504/SRR12975504.sra Written 11017272 spots for SRR12975504/SRR12975504.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172667 ("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: 00:03:48 11017272 reads; of these: 11017272 (100.00%) were unpaired; of these: 5469469 (49.64%) aligned 0 times 1700824 (15.44%) aligned exactly 1 time 3846979 (34.92%) aligned >1 times 50.36% overall alignment rate Time searching: 00:03:48 Overall time: 00:03:48 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_rmdupse_core] 1684147 / 5547803 = 0.3036 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 14:51:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9427697/SRX9427697.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9427697/SRX9427697.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9427697/SRX9427697.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9427697/SRX9427697.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 14:51:06: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:51:06: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:51:11: 1000000 INFO @ Sat, 11 Dec 2021 14:51:15: 2000000 INFO @ Sat, 11 Dec 2021 14:51:20: 3000000 INFO @ Sat, 11 Dec 2021 14:51:24: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:51:24: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:51:24: #1 total tags in treatment: 3863656 INFO @ Sat, 11 Dec 2021 14:51:24: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:51:24: #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 14:51:24: #1 tags after filtering in treatment: 3863656 INFO @ Sat, 11 Dec 2021 14:51:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 14:51:24: #1 finished! INFO @ Sat, 11 Dec 2021 14:51:24: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:51:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:51:25: #2 number of paired peaks: 4410 INFO @ Sat, 11 Dec 2021 14:51:25: start model_add_line... INFO @ Sat, 11 Dec 2021 14:51:25: start X-correlation... INFO @ Sat, 11 Dec 2021 14:51:25: end of X-cor INFO @ Sat, 11 Dec 2021 14:51:25: #2 finished! INFO @ Sat, 11 Dec 2021 14:51:25: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Dec 2021 14:51:25: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 11 Dec 2021 14:51:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9427697/SRX9427697.05_model.r WARNING @ Sat, 11 Dec 2021 14:51:25: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:51:25: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 11 Dec 2021 14:51:25: #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 14:51:25: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:51:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:51:33: #3 Call peaks for each chromosome... 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 14:51:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9427697/SRX9427697.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9427697/SRX9427697.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9427697/SRX9427697.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9427697/SRX9427697.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 14:51:36: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:51:36: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:51:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9427697/SRX9427697.05_peaks.xls INFO @ Sat, 11 Dec 2021 14:51:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9427697/SRX9427697.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:51:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9427697/SRX9427697.05_summits.bed INFO @ Sat, 11 Dec 2021 14:51:37: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5157 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:51:41: 1000000 INFO @ Sat, 11 Dec 2021 14:51:46: 2000000 INFO @ Sat, 11 Dec 2021 14:51:51: 3000000 INFO @ Sat, 11 Dec 2021 14:51:55: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:51:55: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:51:55: #1 total tags in treatment: 3863656 INFO @ Sat, 11 Dec 2021 14:51:55: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:51:55: #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 14:51:55: #1 tags after filtering in treatment: 3863656 INFO @ Sat, 11 Dec 2021 14:51:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 14:51:55: #1 finished! INFO @ Sat, 11 Dec 2021 14:51:55: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:51:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:51:55: #2 number of paired peaks: 4410 INFO @ Sat, 11 Dec 2021 14:51:55: start model_add_line... INFO @ Sat, 11 Dec 2021 14:51:55: start X-correlation... INFO @ Sat, 11 Dec 2021 14:51:55: end of X-cor INFO @ Sat, 11 Dec 2021 14:51:55: #2 finished! INFO @ Sat, 11 Dec 2021 14:51:55: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Dec 2021 14:51:55: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 11 Dec 2021 14:51:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9427697/SRX9427697.10_model.r WARNING @ Sat, 11 Dec 2021 14:51:55: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:51:55: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 11 Dec 2021 14:51:55: #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 14:51:55: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:51:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:52:04: #3 Call peaks for each chromosome... 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 14:52:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9427697/SRX9427697.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9427697/SRX9427697.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9427697/SRX9427697.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9427697/SRX9427697.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 14:52:06: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:52:06: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:52:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9427697/SRX9427697.10_peaks.xls INFO @ Sat, 11 Dec 2021 14:52:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9427697/SRX9427697.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:52:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9427697/SRX9427697.10_summits.bed INFO @ Sat, 11 Dec 2021 14:52:08: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1564 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:52:11: 1000000 INFO @ Sat, 11 Dec 2021 14:52:15: 2000000 INFO @ Sat, 11 Dec 2021 14:52:20: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 14:52:24: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:52:24: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:52:24: #1 total tags in treatment: 3863656 INFO @ Sat, 11 Dec 2021 14:52:24: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:52:24: #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 14:52:24: #1 tags after filtering in treatment: 3863656 INFO @ Sat, 11 Dec 2021 14:52:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 14:52:24: #1 finished! INFO @ Sat, 11 Dec 2021 14:52:24: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:52:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:52:25: #2 number of paired peaks: 4410 INFO @ Sat, 11 Dec 2021 14:52:25: start model_add_line... INFO @ Sat, 11 Dec 2021 14:52:25: start X-correlation... INFO @ Sat, 11 Dec 2021 14:52:25: end of X-cor INFO @ Sat, 11 Dec 2021 14:52:25: #2 finished! INFO @ Sat, 11 Dec 2021 14:52:25: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Dec 2021 14:52:25: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 11 Dec 2021 14:52:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9427697/SRX9427697.20_model.r WARNING @ Sat, 11 Dec 2021 14:52:25: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:52:25: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 11 Dec 2021 14:52:25: #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 14:52:25: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:52:25: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 14:52:33: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:52:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9427697/SRX9427697.20_peaks.xls INFO @ Sat, 11 Dec 2021 14:52:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9427697/SRX9427697.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:52:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9427697/SRX9427697.20_summits.bed INFO @ Sat, 11 Dec 2021 14:52:37: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (592 records, 4 fields): 2 millis CompletedMACS2peakCalling