Job ID = 16437434 SRX = SRX12764396 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 41487088 spots for SRR16562271/SRR16562271.sra Written 41487088 spots for SRR16562271/SRR16562271.sra fastq に変換しました。 bowtie でマッピング中... Your job 16437563 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:03 Multiseed full-index search: 00:06:09 41487088 reads; of these: 41487088 (100.00%) were unpaired; of these: 40175490 (96.84%) aligned 0 times 813878 (1.96%) aligned exactly 1 time 497720 (1.20%) aligned >1 times 3.16% overall alignment rate Time searching: 00:06:13 Overall time: 00:06:13 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] 284757 / 1311598 = 0.2171 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 12:40:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12764396/SRX12764396.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12764396/SRX12764396.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12764396/SRX12764396.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12764396/SRX12764396.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 12:40:18: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:40:18: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:40:25: 1000000 INFO @ Tue, 02 Aug 2022 12:40:25: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 12:40:25: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 12:40:25: #1 total tags in treatment: 1026841 INFO @ Tue, 02 Aug 2022 12:40:25: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:40:25: #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 12:40:25: #1 tags after filtering in treatment: 1026841 INFO @ Tue, 02 Aug 2022 12:40:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 12:40:26: #1 finished! INFO @ Tue, 02 Aug 2022 12:40:26: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:40:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:40:26: #2 number of paired peaks: 1646 INFO @ Tue, 02 Aug 2022 12:40:26: start model_add_line... INFO @ Tue, 02 Aug 2022 12:40:26: start X-correlation... INFO @ Tue, 02 Aug 2022 12:40:26: end of X-cor INFO @ Tue, 02 Aug 2022 12:40:26: #2 finished! INFO @ Tue, 02 Aug 2022 12:40:26: #2 predicted fragment length is 51 bps INFO @ Tue, 02 Aug 2022 12:40:26: #2 alternative fragment length(s) may be 51,473,545 bps INFO @ Tue, 02 Aug 2022 12:40:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12764396/SRX12764396.05_model.r WARNING @ Tue, 02 Aug 2022 12:40:26: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 12:40:26: #2 You may need to consider one of the other alternative d(s): 51,473,545 WARNING @ Tue, 02 Aug 2022 12:40:26: #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 12:40:26: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:40:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:40:29: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:40:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12764396/SRX12764396.05_peaks.xls INFO @ Tue, 02 Aug 2022 12:40:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12764396/SRX12764396.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:40:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12764396/SRX12764396.05_summits.bed INFO @ Tue, 02 Aug 2022 12:40:30: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (767 records, 4 fields): 29 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 12:40:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12764396/SRX12764396.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12764396/SRX12764396.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12764396/SRX12764396.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12764396/SRX12764396.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 12:40:47: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:40:47: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 12:40:53: 1000000 INFO @ Tue, 02 Aug 2022 12:40:54: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 12:40:54: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 12:40:54: #1 total tags in treatment: 1026841 INFO @ Tue, 02 Aug 2022 12:40:54: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:40:54: #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 12:40:54: #1 tags after filtering in treatment: 1026841 INFO @ Tue, 02 Aug 2022 12:40:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 12:40:54: #1 finished! INFO @ Tue, 02 Aug 2022 12:40:54: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:40:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:40:54: #2 number of paired peaks: 1646 INFO @ Tue, 02 Aug 2022 12:40:54: start model_add_line... INFO @ Tue, 02 Aug 2022 12:40:54: start X-correlation... INFO @ Tue, 02 Aug 2022 12:40:55: end of X-cor INFO @ Tue, 02 Aug 2022 12:40:55: #2 finished! INFO @ Tue, 02 Aug 2022 12:40:55: #2 predicted fragment length is 51 bps INFO @ Tue, 02 Aug 2022 12:40:55: #2 alternative fragment length(s) may be 51,473,545 bps INFO @ Tue, 02 Aug 2022 12:40:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12764396/SRX12764396.10_model.r WARNING @ Tue, 02 Aug 2022 12:40:55: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 12:40:55: #2 You may need to consider one of the other alternative d(s): 51,473,545 WARNING @ Tue, 02 Aug 2022 12:40:55: #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 12:40:55: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:40:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 12:40:57: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:40:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12764396/SRX12764396.10_peaks.xls INFO @ Tue, 02 Aug 2022 12:40:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12764396/SRX12764396.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:40:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12764396/SRX12764396.10_summits.bed INFO @ Tue, 02 Aug 2022 12:40:59: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (470 records, 4 fields): 38 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 12:41:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12764396/SRX12764396.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12764396/SRX12764396.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12764396/SRX12764396.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12764396/SRX12764396.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 12:41:17: #1 read tag files... INFO @ Tue, 02 Aug 2022 12:41:17: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 12:41:25: 1000000 INFO @ Tue, 02 Aug 2022 12:41:25: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 12:41:25: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 12:41:25: #1 total tags in treatment: 1026841 INFO @ Tue, 02 Aug 2022 12:41:25: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 12:41:25: #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 12:41:25: #1 tags after filtering in treatment: 1026841 INFO @ Tue, 02 Aug 2022 12:41:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 12:41:25: #1 finished! INFO @ Tue, 02 Aug 2022 12:41:25: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 12:41:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 12:41:25: #2 number of paired peaks: 1646 INFO @ Tue, 02 Aug 2022 12:41:25: start model_add_line... INFO @ Tue, 02 Aug 2022 12:41:25: start X-correlation... INFO @ Tue, 02 Aug 2022 12:41:26: end of X-cor INFO @ Tue, 02 Aug 2022 12:41:26: #2 finished! INFO @ Tue, 02 Aug 2022 12:41:26: #2 predicted fragment length is 51 bps INFO @ Tue, 02 Aug 2022 12:41:26: #2 alternative fragment length(s) may be 51,473,545 bps INFO @ Tue, 02 Aug 2022 12:41:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12764396/SRX12764396.20_model.r WARNING @ Tue, 02 Aug 2022 12:41:26: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 12:41:26: #2 You may need to consider one of the other alternative d(s): 51,473,545 WARNING @ Tue, 02 Aug 2022 12:41:26: #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 12:41:26: #3 Call peaks... INFO @ Tue, 02 Aug 2022 12:41:26: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 12:41:29: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 12:41:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12764396/SRX12764396.20_peaks.xls INFO @ Tue, 02 Aug 2022 12:41:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12764396/SRX12764396.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 12:41:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12764396/SRX12764396.20_summits.bed INFO @ Tue, 02 Aug 2022 12:41:30: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (259 records, 4 fields): 16 millis CompletedMACS2peakCalling