Job ID = 16439286 SRX = SRX15206468 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:56 5613954 reads; of these: 5613954 (100.00%) were unpaired; of these: 156519 (2.79%) aligned 0 times 2523937 (44.96%) aligned exactly 1 time 2933498 (52.25%) aligned >1 times 97.21% overall alignment rate Time searching: 00:01:56 Overall time: 00:01:56 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 661518 / 5457435 = 0.1212 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 14:54:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206468/SRX15206468.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206468/SRX15206468.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206468/SRX15206468.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206468/SRX15206468.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 14:54:22: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:54:22: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:54:30: 1000000 INFO @ Tue, 02 Aug 2022 14:54:37: 2000000 INFO @ Tue, 02 Aug 2022 14:54:45: 3000000 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 14:54:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206468/SRX15206468.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206468/SRX15206468.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206468/SRX15206468.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206468/SRX15206468.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 14:54:52: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:54:52: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:54:53: 4000000 INFO @ Tue, 02 Aug 2022 14:54:59: 1000000 INFO @ Tue, 02 Aug 2022 14:55:00: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:55:00: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:55:00: #1 total tags in treatment: 4795917 INFO @ Tue, 02 Aug 2022 14:55:00: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:55:00: #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 14:55:01: #1 tags after filtering in treatment: 4795819 INFO @ Tue, 02 Aug 2022 14:55:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:55:01: #1 finished! INFO @ Tue, 02 Aug 2022 14:55:01: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:55:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:55:01: #2 number of paired peaks: 2537 INFO @ Tue, 02 Aug 2022 14:55:01: start model_add_line... INFO @ Tue, 02 Aug 2022 14:55:01: start X-correlation... INFO @ Tue, 02 Aug 2022 14:55:01: end of X-cor INFO @ Tue, 02 Aug 2022 14:55:01: #2 finished! INFO @ Tue, 02 Aug 2022 14:55:01: #2 predicted fragment length is 56 bps INFO @ Tue, 02 Aug 2022 14:55:01: #2 alternative fragment length(s) may be 4,56,114 bps INFO @ Tue, 02 Aug 2022 14:55:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206468/SRX15206468.05_model.r WARNING @ Tue, 02 Aug 2022 14:55:01: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:55:01: #2 You may need to consider one of the other alternative d(s): 4,56,114 WARNING @ Tue, 02 Aug 2022 14:55:01: #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 14:55:01: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:55:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:55:06: 2000000 INFO @ Tue, 02 Aug 2022 14:55:11: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:55:14: 3000000 INFO @ Tue, 02 Aug 2022 14:55:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206468/SRX15206468.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:55:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206468/SRX15206468.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:55:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206468/SRX15206468.05_summits.bed INFO @ Tue, 02 Aug 2022 14:55:16: Done! pass1 - making usageList (608 chroms): 1 millis pass2 - checking and writing primary data (2496 records, 4 fields): 67 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 14:55:22: 4000000 INFO @ Tue, 02 Aug 2022 14:55:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206468/SRX15206468.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206468/SRX15206468.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206468/SRX15206468.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206468/SRX15206468.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 14:55:23: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:55:23: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:55:28: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:55:28: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:55:28: #1 total tags in treatment: 4795917 INFO @ Tue, 02 Aug 2022 14:55:28: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:55:28: #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 14:55:29: #1 tags after filtering in treatment: 4795819 INFO @ Tue, 02 Aug 2022 14:55:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:55:29: #1 finished! INFO @ Tue, 02 Aug 2022 14:55:29: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:55:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:55:29: 1000000 INFO @ Tue, 02 Aug 2022 14:55:29: #2 number of paired peaks: 2537 INFO @ Tue, 02 Aug 2022 14:55:29: start model_add_line... INFO @ Tue, 02 Aug 2022 14:55:29: start X-correlation... INFO @ Tue, 02 Aug 2022 14:55:30: end of X-cor INFO @ Tue, 02 Aug 2022 14:55:30: #2 finished! INFO @ Tue, 02 Aug 2022 14:55:30: #2 predicted fragment length is 56 bps INFO @ Tue, 02 Aug 2022 14:55:30: #2 alternative fragment length(s) may be 4,56,114 bps INFO @ Tue, 02 Aug 2022 14:55:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206468/SRX15206468.10_model.r WARNING @ Tue, 02 Aug 2022 14:55:30: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:55:30: #2 You may need to consider one of the other alternative d(s): 4,56,114 WARNING @ Tue, 02 Aug 2022 14:55:30: #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 14:55:30: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:55:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:55:35: 2000000 INFO @ Tue, 02 Aug 2022 14:55:40: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:55:42: 3000000 INFO @ Tue, 02 Aug 2022 14:55:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206468/SRX15206468.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:55:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206468/SRX15206468.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:55:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206468/SRX15206468.10_summits.bed INFO @ Tue, 02 Aug 2022 14:55:45: Done! pass1 - making usageList (478 chroms): 1 millis pass2 - checking and writing primary data (1579 records, 4 fields): 45 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:55:48: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:55:53: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:55:53: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:55:53: #1 total tags in treatment: 4795917 INFO @ Tue, 02 Aug 2022 14:55:53: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:55:53: #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 14:55:54: #1 tags after filtering in treatment: 4795819 INFO @ Tue, 02 Aug 2022 14:55:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:55:54: #1 finished! INFO @ Tue, 02 Aug 2022 14:55:54: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:55:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:55:54: #2 number of paired peaks: 2537 INFO @ Tue, 02 Aug 2022 14:55:54: start model_add_line... INFO @ Tue, 02 Aug 2022 14:55:54: start X-correlation... INFO @ Tue, 02 Aug 2022 14:55:54: end of X-cor INFO @ Tue, 02 Aug 2022 14:55:54: #2 finished! INFO @ Tue, 02 Aug 2022 14:55:54: #2 predicted fragment length is 56 bps INFO @ Tue, 02 Aug 2022 14:55:54: #2 alternative fragment length(s) may be 4,56,114 bps INFO @ Tue, 02 Aug 2022 14:55:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206468/SRX15206468.20_model.r WARNING @ Tue, 02 Aug 2022 14:55:55: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:55:55: #2 You may need to consider one of the other alternative d(s): 4,56,114 WARNING @ Tue, 02 Aug 2022 14:55:55: #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 14:55:55: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:55:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:56:04: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:56:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206468/SRX15206468.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:56:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206468/SRX15206468.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:56:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206468/SRX15206468.20_summits.bed INFO @ Tue, 02 Aug 2022 14:56:09: Done! pass1 - making usageList (316 chroms): 2 millis pass2 - checking and writing primary data (592 records, 4 fields): 22 millis CompletedMACS2peakCalling