Job ID = 16439015 SRX = SRX15206446 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:25:17 prefetch.2.10.7: 1) Downloading 'SRR19139363'... 2022-08-02T05:25:17 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:25:41 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:25:42 prefetch.2.10.7: 'SRR19139363' is valid 2022-08-02T05:25:42 prefetch.2.10.7: 1) 'SRR19139363' was downloaded successfully 2022-08-02T05:25:42 prefetch.2.10.7: 'SRR19139363' has 0 unresolved dependencies Read 11302710 spots for SRR19139363/SRR19139363.sra Written 11302710 spots for SRR19139363/SRR19139363.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439153 ("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: 00:06:29 11302710 reads; of these: 11302710 (100.00%) were unpaired; of these: 1625553 (14.38%) aligned 0 times 5739711 (50.78%) aligned exactly 1 time 3937446 (34.84%) aligned >1 times 85.62% overall alignment rate Time searching: 00:06:29 Overall time: 00:06:29 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] 6826374 / 9677157 = 0.7054 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 14:35:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206446/SRX15206446.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206446/SRX15206446.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206446/SRX15206446.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206446/SRX15206446.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 14:35:01: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:35:01: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:35:07: 1000000 INFO @ Tue, 02 Aug 2022 14:35:13: 2000000 INFO @ Tue, 02 Aug 2022 14:35:19: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 14:35:19: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 14:35:19: #1 total tags in treatment: 2850783 INFO @ Tue, 02 Aug 2022 14:35:19: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:35:19: #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 14:35:19: #1 tags after filtering in treatment: 2850783 INFO @ Tue, 02 Aug 2022 14:35:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:35:19: #1 finished! INFO @ Tue, 02 Aug 2022 14:35:19: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:35:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:35:19: #2 number of paired peaks: 2495 INFO @ Tue, 02 Aug 2022 14:35:19: start model_add_line... INFO @ Tue, 02 Aug 2022 14:35:19: start X-correlation... INFO @ Tue, 02 Aug 2022 14:35:19: end of X-cor INFO @ Tue, 02 Aug 2022 14:35:19: #2 finished! INFO @ Tue, 02 Aug 2022 14:35:19: #2 predicted fragment length is 129 bps INFO @ Tue, 02 Aug 2022 14:35:19: #2 alternative fragment length(s) may be 129 bps INFO @ Tue, 02 Aug 2022 14:35:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206446/SRX15206446.05_model.r WARNING @ Tue, 02 Aug 2022 14:35:19: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:35:19: #2 You may need to consider one of the other alternative d(s): 129 WARNING @ Tue, 02 Aug 2022 14:35:19: #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 14:35:19: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:35:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:35:25: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:35:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206446/SRX15206446.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:35:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206446/SRX15206446.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:35:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206446/SRX15206446.05_summits.bed INFO @ Tue, 02 Aug 2022 14:35:29: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3543 records, 4 fields): 23 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 14:35:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206446/SRX15206446.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206446/SRX15206446.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206446/SRX15206446.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206446/SRX15206446.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 14:35:31: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:35:31: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:35:37: 1000000 INFO @ Tue, 02 Aug 2022 14:35:44: 2000000 INFO @ Tue, 02 Aug 2022 14:35:50: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 14:35:50: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 14:35:50: #1 total tags in treatment: 2850783 INFO @ Tue, 02 Aug 2022 14:35:50: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:35:50: #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 14:35:50: #1 tags after filtering in treatment: 2850783 INFO @ Tue, 02 Aug 2022 14:35:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:35:50: #1 finished! INFO @ Tue, 02 Aug 2022 14:35:50: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:35:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:35:50: #2 number of paired peaks: 2495 INFO @ Tue, 02 Aug 2022 14:35:50: start model_add_line... INFO @ Tue, 02 Aug 2022 14:35:50: start X-correlation... INFO @ Tue, 02 Aug 2022 14:35:50: end of X-cor INFO @ Tue, 02 Aug 2022 14:35:50: #2 finished! INFO @ Tue, 02 Aug 2022 14:35:50: #2 predicted fragment length is 129 bps INFO @ Tue, 02 Aug 2022 14:35:50: #2 alternative fragment length(s) may be 129 bps INFO @ Tue, 02 Aug 2022 14:35:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206446/SRX15206446.10_model.r WARNING @ Tue, 02 Aug 2022 14:35:50: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:35:50: #2 You may need to consider one of the other alternative d(s): 129 WARNING @ Tue, 02 Aug 2022 14:35:50: #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 14:35:50: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:35:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:35:56: #3 Call peaks for each chromosome... 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 14:36:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206446/SRX15206446.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:36:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206446/SRX15206446.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:36:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206446/SRX15206446.10_summits.bed INFO @ Tue, 02 Aug 2022 14:36:00: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1060 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:36:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206446/SRX15206446.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206446/SRX15206446.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206446/SRX15206446.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206446/SRX15206446.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 14:36:01: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:36:01: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:36:08: 1000000 INFO @ Tue, 02 Aug 2022 14:36:14: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:36:19: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 14:36:19: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 14:36:19: #1 total tags in treatment: 2850783 INFO @ Tue, 02 Aug 2022 14:36:19: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:36:19: #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 14:36:19: #1 tags after filtering in treatment: 2850783 INFO @ Tue, 02 Aug 2022 14:36:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:36:19: #1 finished! INFO @ Tue, 02 Aug 2022 14:36:19: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:36:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:36:20: #2 number of paired peaks: 2495 INFO @ Tue, 02 Aug 2022 14:36:20: start model_add_line... INFO @ Tue, 02 Aug 2022 14:36:20: start X-correlation... INFO @ Tue, 02 Aug 2022 14:36:20: end of X-cor INFO @ Tue, 02 Aug 2022 14:36:20: #2 finished! INFO @ Tue, 02 Aug 2022 14:36:20: #2 predicted fragment length is 129 bps INFO @ Tue, 02 Aug 2022 14:36:20: #2 alternative fragment length(s) may be 129 bps INFO @ Tue, 02 Aug 2022 14:36:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206446/SRX15206446.20_model.r WARNING @ Tue, 02 Aug 2022 14:36:20: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:36:20: #2 You may need to consider one of the other alternative d(s): 129 WARNING @ Tue, 02 Aug 2022 14:36:20: #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 14:36:20: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:36:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:36:26: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:36:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206446/SRX15206446.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:36:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206446/SRX15206446.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:36:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206446/SRX15206446.20_summits.bed INFO @ Tue, 02 Aug 2022 14:36:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (210 records, 4 fields): 24 millis CompletedMACS2peakCalling