Job ID = 16437342 SRX = SRX12764388 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 31652850 spots for SRR16562265/SRR16562265.sra Written 31652850 spots for SRR16562265/SRR16562265.sra fastq に変換しました。 bowtie でマッピング中... Your job 16437448 ("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: 00:03:43 31652850 reads; of these: 31652850 (100.00%) were unpaired; of these: 31086953 (98.21%) aligned 0 times 214289 (0.68%) aligned exactly 1 time 351608 (1.11%) aligned >1 times 1.79% overall alignment rate Time searching: 00:03:43 Overall time: 00:03:43 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] 105053 / 565897 = 0.1856 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 12:27:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12764388/SRX12764388.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12764388/SRX12764388.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12764388/SRX12764388.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12764388/SRX12764388.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 @ Tue, 02 Aug 2022 12:27:56: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:27:56: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:28:01: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 12:28:01: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 12:28:01: #1 total tags in treatment: 460844 INFO @ Tue, 02 Aug 2022 12:28:01: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:28:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 12:28:01: #1 tags after filtering in treatment: 460844 INFO @ Tue, 02 Aug 2022 12:28:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 12:28:01: #1 finished! INFO @ Tue, 02 Aug 2022 12:28:01: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:28:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:28:01: #2 number of paired peaks: 1889 INFO @ Tue, 02 Aug 2022 12:28:01: start model_add_line... INFO @ Tue, 02 Aug 2022 12:28:01: start X-correlation... INFO @ Tue, 02 Aug 2022 12:28:01: end of X-cor INFO @ Tue, 02 Aug 2022 12:28:01: #2 finished! INFO @ Tue, 02 Aug 2022 12:28:01: #2 predicted fragment length is 49 bps INFO @ Tue, 02 Aug 2022 12:28:01: #2 alternative fragment length(s) may be 49,267,425,521,565 bps INFO @ Tue, 02 Aug 2022 12:28:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12764388/SRX12764388.05_model.r WARNING @ Tue, 02 Aug 2022 12:28:01: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 12:28:01: #2 You may need to consider one of the other alternative d(s): 49,267,425,521,565 WARNING @ Tue, 02 Aug 2022 12:28:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 12:28:01: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:28:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:28:02: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:28:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12764388/SRX12764388.05_peaks.xls INFO @ Tue, 02 Aug 2022 12:28:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12764388/SRX12764388.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:28:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12764388/SRX12764388.05_summits.bed INFO @ Tue, 02 Aug 2022 12:28:03: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (924 records, 4 fields): 103 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 12:28:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12764388/SRX12764388.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12764388/SRX12764388.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12764388/SRX12764388.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12764388/SRX12764388.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 @ Tue, 02 Aug 2022 12:28:26: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:28:26: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:28:30: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 12:28:30: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 12:28:30: #1 total tags in treatment: 460844 INFO @ Tue, 02 Aug 2022 12:28:30: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:28:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 12:28:30: #1 tags after filtering in treatment: 460844 INFO @ Tue, 02 Aug 2022 12:28:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 12:28:30: #1 finished! INFO @ Tue, 02 Aug 2022 12:28:30: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:28:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:28:30: #2 number of paired peaks: 1889 INFO @ Tue, 02 Aug 2022 12:28:30: start model_add_line... INFO @ Tue, 02 Aug 2022 12:28:30: start X-correlation... INFO @ Tue, 02 Aug 2022 12:28:30: end of X-cor INFO @ Tue, 02 Aug 2022 12:28:30: #2 finished! INFO @ Tue, 02 Aug 2022 12:28:30: #2 predicted fragment length is 49 bps INFO @ Tue, 02 Aug 2022 12:28:30: #2 alternative fragment length(s) may be 49,267,425,521,565 bps INFO @ Tue, 02 Aug 2022 12:28:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12764388/SRX12764388.10_model.r WARNING @ Tue, 02 Aug 2022 12:28:30: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 12:28:30: #2 You may need to consider one of the other alternative d(s): 49,267,425,521,565 WARNING @ Tue, 02 Aug 2022 12:28:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 12:28:30: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:28:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:28:31: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:28:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12764388/SRX12764388.10_peaks.xls INFO @ Tue, 02 Aug 2022 12:28:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12764388/SRX12764388.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:28:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12764388/SRX12764388.10_summits.bed INFO @ Tue, 02 Aug 2022 12:28:32: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (544 records, 4 fields): 106 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 12:28:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12764388/SRX12764388.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12764388/SRX12764388.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12764388/SRX12764388.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12764388/SRX12764388.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 @ Tue, 02 Aug 2022 12:28:56: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:28:56: #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 @ Tue, 02 Aug 2022 12:29:00: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 12:29:00: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 12:29:00: #1 total tags in treatment: 460844 INFO @ Tue, 02 Aug 2022 12:29:00: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:29:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 12:29:00: #1 tags after filtering in treatment: 460844 INFO @ Tue, 02 Aug 2022 12:29:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 12:29:00: #1 finished! INFO @ Tue, 02 Aug 2022 12:29:00: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:29:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:29:00: #2 number of paired peaks: 1889 INFO @ Tue, 02 Aug 2022 12:29:00: start model_add_line... INFO @ Tue, 02 Aug 2022 12:29:00: start X-correlation... INFO @ Tue, 02 Aug 2022 12:29:00: end of X-cor INFO @ Tue, 02 Aug 2022 12:29:00: #2 finished! INFO @ Tue, 02 Aug 2022 12:29:00: #2 predicted fragment length is 49 bps INFO @ Tue, 02 Aug 2022 12:29:00: #2 alternative fragment length(s) may be 49,267,425,521,565 bps INFO @ Tue, 02 Aug 2022 12:29:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12764388/SRX12764388.20_model.r WARNING @ Tue, 02 Aug 2022 12:29:00: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 12:29:00: #2 You may need to consider one of the other alternative d(s): 49,267,425,521,565 WARNING @ Tue, 02 Aug 2022 12:29:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 12:29:00: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:29:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:29:01: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:29:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12764388/SRX12764388.20_peaks.xls INFO @ Tue, 02 Aug 2022 12:29:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12764388/SRX12764388.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:29:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12764388/SRX12764388.20_summits.bed INFO @ Tue, 02 Aug 2022 12:29:02: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (278 records, 4 fields): 87 millis CompletedMACS2peakCalling