Job ID = 14171359 SRX = SRX8512934 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 1509913 spots for SRR11969180/SRR11969180.sra Written 1509913 spots for SRR11969180/SRR11969180.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171811 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:58 1509913 reads; of these: 1509913 (100.00%) were unpaired; of these: 215 (0.01%) aligned 0 times 1033346 (68.44%) aligned exactly 1 time 476352 (31.55%) aligned >1 times 99.99% overall alignment rate Time searching: 00:00:59 Overall time: 00:00:59 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] 593184 / 1509698 = 0.3929 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 11:25:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8512934/SRX8512934.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8512934/SRX8512934.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8512934/SRX8512934.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8512934/SRX8512934.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 11:25:42: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:25:42: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:25:49: #1 tag size is determined as 142 bps INFO @ Sat, 11 Dec 2021 11:25:49: #1 tag size = 142 INFO @ Sat, 11 Dec 2021 11:25:49: #1 total tags in treatment: 916514 INFO @ Sat, 11 Dec 2021 11:25:49: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:25:49: #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 11:25:49: #1 tags after filtering in treatment: 916514 INFO @ Sat, 11 Dec 2021 11:25:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:25:49: #1 finished! INFO @ Sat, 11 Dec 2021 11:25:49: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:25:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:25:50: #2 number of paired peaks: 5384 INFO @ Sat, 11 Dec 2021 11:25:50: start model_add_line... INFO @ Sat, 11 Dec 2021 11:25:50: start X-correlation... INFO @ Sat, 11 Dec 2021 11:25:50: end of X-cor INFO @ Sat, 11 Dec 2021 11:25:50: #2 finished! INFO @ Sat, 11 Dec 2021 11:25:50: #2 predicted fragment length is 156 bps INFO @ Sat, 11 Dec 2021 11:25:50: #2 alternative fragment length(s) may be 156 bps INFO @ Sat, 11 Dec 2021 11:25:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8512934/SRX8512934.05_model.r WARNING @ Sat, 11 Dec 2021 11:25:50: #2 Since the d (156) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:25:50: #2 You may need to consider one of the other alternative d(s): 156 WARNING @ Sat, 11 Dec 2021 11:25:50: #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 11:25:50: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:25:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:25:52: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:25:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8512934/SRX8512934.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:25:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8512934/SRX8512934.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:25:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8512934/SRX8512934.05_summits.bed INFO @ Sat, 11 Dec 2021 11:25:53: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1562 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 11:26:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8512934/SRX8512934.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8512934/SRX8512934.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8512934/SRX8512934.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8512934/SRX8512934.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 11:26:12: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:26:12: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:26:19: #1 tag size is determined as 142 bps INFO @ Sat, 11 Dec 2021 11:26:19: #1 tag size = 142 INFO @ Sat, 11 Dec 2021 11:26:19: #1 total tags in treatment: 916514 INFO @ Sat, 11 Dec 2021 11:26:19: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:26:19: #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 11:26:19: #1 tags after filtering in treatment: 916514 INFO @ Sat, 11 Dec 2021 11:26:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:26:19: #1 finished! INFO @ Sat, 11 Dec 2021 11:26:19: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:26:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:26:19: #2 number of paired peaks: 5384 INFO @ Sat, 11 Dec 2021 11:26:19: start model_add_line... INFO @ Sat, 11 Dec 2021 11:26:19: start X-correlation... INFO @ Sat, 11 Dec 2021 11:26:19: end of X-cor INFO @ Sat, 11 Dec 2021 11:26:19: #2 finished! INFO @ Sat, 11 Dec 2021 11:26:19: #2 predicted fragment length is 156 bps INFO @ Sat, 11 Dec 2021 11:26:19: #2 alternative fragment length(s) may be 156 bps INFO @ Sat, 11 Dec 2021 11:26:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8512934/SRX8512934.10_model.r WARNING @ Sat, 11 Dec 2021 11:26:19: #2 Since the d (156) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:26:19: #2 You may need to consider one of the other alternative d(s): 156 WARNING @ Sat, 11 Dec 2021 11:26:19: #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 11:26:19: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:26:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:26:21: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:26:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8512934/SRX8512934.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:26:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8512934/SRX8512934.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:26:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8512934/SRX8512934.10_summits.bed INFO @ Sat, 11 Dec 2021 11:26:22: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (507 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 11:26:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8512934/SRX8512934.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8512934/SRX8512934.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8512934/SRX8512934.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8512934/SRX8512934.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 11:26:42: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:26:42: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:26:49: #1 tag size is determined as 142 bps INFO @ Sat, 11 Dec 2021 11:26:49: #1 tag size = 142 INFO @ Sat, 11 Dec 2021 11:26:49: #1 total tags in treatment: 916514 INFO @ Sat, 11 Dec 2021 11:26:49: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:26:49: #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 11:26:49: #1 tags after filtering in treatment: 916514 INFO @ Sat, 11 Dec 2021 11:26:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 11:26:49: #1 finished! INFO @ Sat, 11 Dec 2021 11:26:49: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:26:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:26:49: #2 number of paired peaks: 5384 INFO @ Sat, 11 Dec 2021 11:26:49: start model_add_line... INFO @ Sat, 11 Dec 2021 11:26:49: start X-correlation... INFO @ Sat, 11 Dec 2021 11:26:49: end of X-cor INFO @ Sat, 11 Dec 2021 11:26:49: #2 finished! INFO @ Sat, 11 Dec 2021 11:26:49: #2 predicted fragment length is 156 bps INFO @ Sat, 11 Dec 2021 11:26:49: #2 alternative fragment length(s) may be 156 bps INFO @ Sat, 11 Dec 2021 11:26:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8512934/SRX8512934.20_model.r WARNING @ Sat, 11 Dec 2021 11:26:49: #2 Since the d (156) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 11:26:49: #2 You may need to consider one of the other alternative d(s): 156 WARNING @ Sat, 11 Dec 2021 11:26:49: #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 11:26:49: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:26:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:26:51: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:26:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8512934/SRX8512934.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:26:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8512934/SRX8512934.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:26:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8512934/SRX8512934.20_summits.bed INFO @ Sat, 11 Dec 2021 11:26:52: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (218 records, 4 fields): 1 millis CompletedMACS2peakCalling