Job ID = 14172183 SRX = SRX9427691 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 13142643 spots for SRR12975498/SRR12975498.sra Written 13142643 spots for SRR12975498/SRR12975498.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172646 ("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: 00:02:32 13142643 reads; of these: 13142643 (100.00%) were unpaired; of these: 11395789 (86.71%) aligned 0 times 592646 (4.51%) aligned exactly 1 time 1154208 (8.78%) aligned >1 times 13.29% overall alignment rate Time searching: 00:02:32 Overall time: 00:02:32 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] 460049 / 1746854 = 0.2634 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 14:46:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9427691/SRX9427691.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9427691/SRX9427691.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9427691/SRX9427691.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9427691/SRX9427691.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 14:46:02: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:46:02: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:46:10: 1000000 INFO @ Sat, 11 Dec 2021 14:46:12: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:46:12: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:46:12: #1 total tags in treatment: 1286805 INFO @ Sat, 11 Dec 2021 14:46:12: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:46:12: #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 14:46:12: #1 tags after filtering in treatment: 1286805 INFO @ Sat, 11 Dec 2021 14:46:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 14:46:12: #1 finished! INFO @ Sat, 11 Dec 2021 14:46:12: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:46:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:46:13: #2 number of paired peaks: 4889 INFO @ Sat, 11 Dec 2021 14:46:13: start model_add_line... INFO @ Sat, 11 Dec 2021 14:46:13: start X-correlation... INFO @ Sat, 11 Dec 2021 14:46:13: end of X-cor INFO @ Sat, 11 Dec 2021 14:46:13: #2 finished! INFO @ Sat, 11 Dec 2021 14:46:13: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Dec 2021 14:46:13: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 11 Dec 2021 14:46:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9427691/SRX9427691.05_model.r WARNING @ Sat, 11 Dec 2021 14:46:13: #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 14:46:13: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 11 Dec 2021 14:46:13: #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 14:46:13: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:46:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:46:15: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:46:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9427691/SRX9427691.05_peaks.xls INFO @ Sat, 11 Dec 2021 14:46:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9427691/SRX9427691.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:46:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9427691/SRX9427691.05_summits.bed INFO @ Sat, 11 Dec 2021 14:46:17: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (1484 records, 4 fields): 6 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 14:46:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9427691/SRX9427691.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9427691/SRX9427691.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9427691/SRX9427691.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9427691/SRX9427691.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 14:46:32: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:46:32: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:46:38: 1000000 INFO @ Sat, 11 Dec 2021 14:46:39: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:46:39: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:46:39: #1 total tags in treatment: 1286805 INFO @ Sat, 11 Dec 2021 14:46:39: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:46:39: #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 14:46:39: #1 tags after filtering in treatment: 1286805 INFO @ Sat, 11 Dec 2021 14:46:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 14:46:39: #1 finished! INFO @ Sat, 11 Dec 2021 14:46:39: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:46:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:46:40: #2 number of paired peaks: 4889 INFO @ Sat, 11 Dec 2021 14:46:40: start model_add_line... INFO @ Sat, 11 Dec 2021 14:46:40: start X-correlation... INFO @ Sat, 11 Dec 2021 14:46:40: end of X-cor INFO @ Sat, 11 Dec 2021 14:46:40: #2 finished! INFO @ Sat, 11 Dec 2021 14:46:40: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Dec 2021 14:46:40: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 11 Dec 2021 14:46:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9427691/SRX9427691.10_model.r WARNING @ Sat, 11 Dec 2021 14:46:40: #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 14:46:40: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 11 Dec 2021 14:46:40: #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 14:46:40: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:46:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:46:42: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:46:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9427691/SRX9427691.10_peaks.xls INFO @ Sat, 11 Dec 2021 14:46:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9427691/SRX9427691.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:46:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9427691/SRX9427691.10_summits.bed INFO @ Sat, 11 Dec 2021 14:46:44: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (696 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 14:47:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9427691/SRX9427691.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9427691/SRX9427691.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9427691/SRX9427691.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9427691/SRX9427691.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 14:47:02: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:47:02: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:47:08: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 14:47:10: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:47:10: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:47:10: #1 total tags in treatment: 1286805 INFO @ Sat, 11 Dec 2021 14:47:10: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:47:10: #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 14:47:10: #1 tags after filtering in treatment: 1286805 INFO @ Sat, 11 Dec 2021 14:47:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 14:47:10: #1 finished! INFO @ Sat, 11 Dec 2021 14:47:10: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:47:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:47:10: #2 number of paired peaks: 4889 INFO @ Sat, 11 Dec 2021 14:47:10: start model_add_line... INFO @ Sat, 11 Dec 2021 14:47:10: start X-correlation... INFO @ Sat, 11 Dec 2021 14:47:10: end of X-cor INFO @ Sat, 11 Dec 2021 14:47:10: #2 finished! INFO @ Sat, 11 Dec 2021 14:47:10: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Dec 2021 14:47:10: #2 alternative fragment length(s) may be 52 bps INFO @ Sat, 11 Dec 2021 14:47:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9427691/SRX9427691.20_model.r WARNING @ Sat, 11 Dec 2021 14:47:10: #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 14:47:10: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Sat, 11 Dec 2021 14:47:10: #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 14:47:10: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:47:10: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 14:47:13: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:47:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9427691/SRX9427691.20_peaks.xls INFO @ Sat, 11 Dec 2021 14:47:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9427691/SRX9427691.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:47:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9427691/SRX9427691.20_summits.bed INFO @ Sat, 11 Dec 2021 14:47:14: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (328 records, 4 fields): 3 millis CompletedMACS2peakCalling