Job ID = 16438991 SRX = SRX15206434 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:20:24 prefetch.2.10.7: 1) Downloading 'SRR19139377'... 2022-08-02T05:20:24 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:20:39 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:20:40 prefetch.2.10.7: 'SRR19139377' is valid 2022-08-02T05:20:40 prefetch.2.10.7: 1) 'SRR19139377' was downloaded successfully 2022-08-02T05:20:40 prefetch.2.10.7: 'SRR19139377' has 0 unresolved dependencies Read 8433765 spots for SRR19139377/SRR19139377.sra Written 8433765 spots for SRR19139377/SRR19139377.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439135 ("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: 00:04:35 8433765 reads; of these: 8433765 (100.00%) were unpaired; of these: 147069 (1.74%) aligned 0 times 2786868 (33.04%) aligned exactly 1 time 5499828 (65.21%) aligned >1 times 98.26% overall alignment rate Time searching: 00:04:35 Overall time: 00:04:35 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] 884251 / 8286696 = 0.1067 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 14:28:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206434/SRX15206434.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206434/SRX15206434.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206434/SRX15206434.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206434/SRX15206434.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 14:28:14: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:28:14: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:28:22: 1000000 INFO @ Tue, 02 Aug 2022 14:28:29: 2000000 INFO @ Tue, 02 Aug 2022 14:28:36: 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 14:28:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206434/SRX15206434.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206434/SRX15206434.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206434/SRX15206434.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206434/SRX15206434.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 14:28:44: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:28:44: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:28:44: 4000000 INFO @ Tue, 02 Aug 2022 14:28:51: 1000000 INFO @ Tue, 02 Aug 2022 14:28:52: 5000000 INFO @ Tue, 02 Aug 2022 14:28:58: 2000000 INFO @ Tue, 02 Aug 2022 14:29:00: 6000000 INFO @ Tue, 02 Aug 2022 14:29:05: 3000000 INFO @ Tue, 02 Aug 2022 14:29:07: 7000000 INFO @ Tue, 02 Aug 2022 14:29:10: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:29:10: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:29:10: #1 total tags in treatment: 7402445 INFO @ Tue, 02 Aug 2022 14:29:10: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:29:10: #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 14:29:11: #1 tags after filtering in treatment: 7402445 INFO @ Tue, 02 Aug 2022 14:29:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:29:11: #1 finished! INFO @ Tue, 02 Aug 2022 14:29:11: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:29:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:29:11: #2 number of paired peaks: 3906 INFO @ Tue, 02 Aug 2022 14:29:11: start model_add_line... INFO @ Tue, 02 Aug 2022 14:29:11: start X-correlation... INFO @ Tue, 02 Aug 2022 14:29:11: end of X-cor INFO @ Tue, 02 Aug 2022 14:29:11: #2 finished! INFO @ Tue, 02 Aug 2022 14:29:11: #2 predicted fragment length is 142 bps INFO @ Tue, 02 Aug 2022 14:29:11: #2 alternative fragment length(s) may be 4,142 bps INFO @ Tue, 02 Aug 2022 14:29:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206434/SRX15206434.05_model.r WARNING @ Tue, 02 Aug 2022 14:29:11: #2 Since the d (142) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:29:11: #2 You may need to consider one of the other alternative d(s): 4,142 WARNING @ Tue, 02 Aug 2022 14:29:11: #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 14:29:11: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:29:11: #3 Pre-compute pvalue-qvalue table... 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 14:29:12: 4000000 INFO @ Tue, 02 Aug 2022 14:29:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206434/SRX15206434.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206434/SRX15206434.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206434/SRX15206434.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206434/SRX15206434.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 14:29:14: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:29:14: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:29:19: 5000000 INFO @ Tue, 02 Aug 2022 14:29:22: 1000000 INFO @ Tue, 02 Aug 2022 14:29:27: 6000000 INFO @ Tue, 02 Aug 2022 14:29:27: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:29:30: 2000000 INFO @ Tue, 02 Aug 2022 14:29:34: 7000000 INFO @ Tue, 02 Aug 2022 14:29:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206434/SRX15206434.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:29:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206434/SRX15206434.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:29:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206434/SRX15206434.05_summits.bed INFO @ Tue, 02 Aug 2022 14:29:36: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (7305 records, 4 fields): 170 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:29:36: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:29:36: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:29:36: #1 total tags in treatment: 7402445 INFO @ Tue, 02 Aug 2022 14:29:36: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:29:36: #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 14:29:37: #1 tags after filtering in treatment: 7402445 INFO @ Tue, 02 Aug 2022 14:29:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:29:37: #1 finished! INFO @ Tue, 02 Aug 2022 14:29:37: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:29:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:29:37: #2 number of paired peaks: 3906 INFO @ Tue, 02 Aug 2022 14:29:37: start model_add_line... INFO @ Tue, 02 Aug 2022 14:29:37: start X-correlation... INFO @ Tue, 02 Aug 2022 14:29:37: end of X-cor INFO @ Tue, 02 Aug 2022 14:29:37: #2 finished! INFO @ Tue, 02 Aug 2022 14:29:37: #2 predicted fragment length is 142 bps INFO @ Tue, 02 Aug 2022 14:29:37: #2 alternative fragment length(s) may be 4,142 bps INFO @ Tue, 02 Aug 2022 14:29:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206434/SRX15206434.10_model.r WARNING @ Tue, 02 Aug 2022 14:29:37: #2 Since the d (142) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:29:37: #2 You may need to consider one of the other alternative d(s): 4,142 WARNING @ Tue, 02 Aug 2022 14:29:37: #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 14:29:37: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:29:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:29:38: 3000000 INFO @ Tue, 02 Aug 2022 14:29:45: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:29:53: 5000000 INFO @ Tue, 02 Aug 2022 14:29:54: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:30:00: 6000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:30:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206434/SRX15206434.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:30:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206434/SRX15206434.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:30:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206434/SRX15206434.10_summits.bed INFO @ Tue, 02 Aug 2022 14:30:03: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2764 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:30:08: 7000000 INFO @ Tue, 02 Aug 2022 14:30:10: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:30:10: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:30:10: #1 total tags in treatment: 7402445 INFO @ Tue, 02 Aug 2022 14:30:10: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:30:10: #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 14:30:10: #1 tags after filtering in treatment: 7402445 INFO @ Tue, 02 Aug 2022 14:30:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:30:10: #1 finished! INFO @ Tue, 02 Aug 2022 14:30:10: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:30:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:30:11: #2 number of paired peaks: 3906 INFO @ Tue, 02 Aug 2022 14:30:11: start model_add_line... INFO @ Tue, 02 Aug 2022 14:30:11: start X-correlation... INFO @ Tue, 02 Aug 2022 14:30:11: end of X-cor INFO @ Tue, 02 Aug 2022 14:30:11: #2 finished! INFO @ Tue, 02 Aug 2022 14:30:11: #2 predicted fragment length is 142 bps INFO @ Tue, 02 Aug 2022 14:30:11: #2 alternative fragment length(s) may be 4,142 bps INFO @ Tue, 02 Aug 2022 14:30:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206434/SRX15206434.20_model.r WARNING @ Tue, 02 Aug 2022 14:30:11: #2 Since the d (142) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:30:11: #2 You may need to consider one of the other alternative d(s): 4,142 WARNING @ Tue, 02 Aug 2022 14:30:11: #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 14:30:11: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:30:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:30:28: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:30:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206434/SRX15206434.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:30:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206434/SRX15206434.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:30:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206434/SRX15206434.20_summits.bed INFO @ Tue, 02 Aug 2022 14:30:36: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (759 records, 4 fields): 39 millis CompletedMACS2peakCalling