Job ID = 16438922 SRX = SRX15206518 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:10:00 prefetch.2.10.7: 1) Downloading 'SRR19139274'... 2022-08-02T05:10:00 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:10:22 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:10:23 prefetch.2.10.7: 'SRR19139274' is valid 2022-08-02T05:10:23 prefetch.2.10.7: 1) 'SRR19139274' was downloaded successfully 2022-08-02T05:10:23 prefetch.2.10.7: 'SRR19139274' has 0 unresolved dependencies Read 8856811 spots for SRR19139274/SRR19139274.sra Written 8856811 spots for SRR19139274/SRR19139274.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438978 ("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: 00:05:32 8856811 reads; of these: 8856811 (100.00%) were unpaired; of these: 690742 (7.80%) aligned 0 times 6739819 (76.10%) aligned exactly 1 time 1426250 (16.10%) aligned >1 times 92.20% overall alignment rate Time searching: 00:05:32 Overall time: 00:05:32 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] 6699717 / 8166069 = 0.8204 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 14:19:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206518/SRX15206518.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206518/SRX15206518.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206518/SRX15206518.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206518/SRX15206518.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 14:19:07: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:19:07: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:19:20: 1000000 INFO @ Tue, 02 Aug 2022 14:19:25: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 14:19:25: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 14:19:25: #1 total tags in treatment: 1466352 INFO @ Tue, 02 Aug 2022 14:19:25: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:19:25: #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 14:19:25: #1 tags after filtering in treatment: 1466352 INFO @ Tue, 02 Aug 2022 14:19:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:19:25: #1 finished! INFO @ Tue, 02 Aug 2022 14:19:25: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:19:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:19:26: #2 number of paired peaks: 1724 INFO @ Tue, 02 Aug 2022 14:19:26: start model_add_line... INFO @ Tue, 02 Aug 2022 14:19:26: start X-correlation... INFO @ Tue, 02 Aug 2022 14:19:26: end of X-cor INFO @ Tue, 02 Aug 2022 14:19:26: #2 finished! INFO @ Tue, 02 Aug 2022 14:19:26: #2 predicted fragment length is 157 bps INFO @ Tue, 02 Aug 2022 14:19:26: #2 alternative fragment length(s) may be 157 bps INFO @ Tue, 02 Aug 2022 14:19:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206518/SRX15206518.05_model.r WARNING @ Tue, 02 Aug 2022 14:19:26: #2 Since the d (157) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:19:26: #2 You may need to consider one of the other alternative d(s): 157 WARNING @ Tue, 02 Aug 2022 14:19:26: #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 14:19:26: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:19:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:19:31: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:19:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206518/SRX15206518.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:19:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206518/SRX15206518.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:19:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206518/SRX15206518.05_summits.bed INFO @ Tue, 02 Aug 2022 14:19:34: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (1364 records, 4 fields): 97 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 14:19:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206518/SRX15206518.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206518/SRX15206518.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206518/SRX15206518.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206518/SRX15206518.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 14:19:37: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:19:37: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:19:49: 1000000 INFO @ Tue, 02 Aug 2022 14:19:55: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 14:19:55: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 14:19:55: #1 total tags in treatment: 1466352 INFO @ Tue, 02 Aug 2022 14:19:55: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:19:55: #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 14:19:55: #1 tags after filtering in treatment: 1466352 INFO @ Tue, 02 Aug 2022 14:19:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:19:55: #1 finished! INFO @ Tue, 02 Aug 2022 14:19:55: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:19:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:19:55: #2 number of paired peaks: 1724 INFO @ Tue, 02 Aug 2022 14:19:55: start model_add_line... INFO @ Tue, 02 Aug 2022 14:19:55: start X-correlation... INFO @ Tue, 02 Aug 2022 14:19:55: end of X-cor INFO @ Tue, 02 Aug 2022 14:19:55: #2 finished! INFO @ Tue, 02 Aug 2022 14:19:55: #2 predicted fragment length is 157 bps INFO @ Tue, 02 Aug 2022 14:19:55: #2 alternative fragment length(s) may be 157 bps INFO @ Tue, 02 Aug 2022 14:19:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206518/SRX15206518.10_model.r WARNING @ Tue, 02 Aug 2022 14:19:55: #2 Since the d (157) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:19:55: #2 You may need to consider one of the other alternative d(s): 157 WARNING @ Tue, 02 Aug 2022 14:19:55: #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 14:19:55: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:19:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:20:00: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:20:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206518/SRX15206518.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:20:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206518/SRX15206518.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:20:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206518/SRX15206518.10_summits.bed INFO @ Tue, 02 Aug 2022 14:20:03: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (416 records, 4 fields): 34 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 14:20:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206518/SRX15206518.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206518/SRX15206518.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206518/SRX15206518.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206518/SRX15206518.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 14:20:07: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:20:07: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:20:19: 1000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:20:25: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 14:20:25: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 14:20:25: #1 total tags in treatment: 1466352 INFO @ Tue, 02 Aug 2022 14:20:25: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:20:25: #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 14:20:25: #1 tags after filtering in treatment: 1466352 INFO @ Tue, 02 Aug 2022 14:20:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:20:25: #1 finished! INFO @ Tue, 02 Aug 2022 14:20:25: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:20:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:20:25: #2 number of paired peaks: 1724 INFO @ Tue, 02 Aug 2022 14:20:25: start model_add_line... INFO @ Tue, 02 Aug 2022 14:20:25: start X-correlation... INFO @ Tue, 02 Aug 2022 14:20:25: end of X-cor INFO @ Tue, 02 Aug 2022 14:20:25: #2 finished! INFO @ Tue, 02 Aug 2022 14:20:25: #2 predicted fragment length is 157 bps INFO @ Tue, 02 Aug 2022 14:20:25: #2 alternative fragment length(s) may be 157 bps INFO @ Tue, 02 Aug 2022 14:20:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206518/SRX15206518.20_model.r WARNING @ Tue, 02 Aug 2022 14:20:25: #2 Since the d (157) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:20:25: #2 You may need to consider one of the other alternative d(s): 157 WARNING @ Tue, 02 Aug 2022 14:20:25: #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 14:20:25: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:20:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:20:30: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:20:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206518/SRX15206518.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:20:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206518/SRX15206518.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:20:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206518/SRX15206518.20_summits.bed INFO @ Tue, 02 Aug 2022 14:20:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (70 records, 4 fields): 21 millis CompletedMACS2peakCalling