Job ID = 16438949 SRX = SRX15206524 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:14:08 prefetch.2.10.7: 1) Downloading 'SRR19139268'... 2022-08-02T05:14:08 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:15:31 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:15:31 prefetch.2.10.7: 1) 'SRR19139268' was downloaded successfully 2022-08-02T05:15:31 prefetch.2.10.7: 'SRR19139268' has 0 unresolved dependencies Read 23752458 spots for SRR19139268/SRR19139268.sra Written 23752458 spots for SRR19139268/SRR19139268.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439165 ("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: 00:20:33 23752458 reads; of these: 23752458 (100.00%) were unpaired; of these: 1458863 (6.14%) aligned 0 times 12210338 (51.41%) aligned exactly 1 time 10083257 (42.45%) aligned >1 times 93.86% overall alignment rate Time searching: 00:20:33 Overall time: 00:20:33 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_sort_core] merging from 20 files... [bam_rmdupse_core] 15502708 / 22293595 = 0.6954 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 14:46:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206524/SRX15206524.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206524/SRX15206524.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206524/SRX15206524.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206524/SRX15206524.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 14:46:45: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:46:45: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:46:53: 1000000 INFO @ Tue, 02 Aug 2022 14:47:02: 2000000 INFO @ Tue, 02 Aug 2022 14:47:10: 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 14:47:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206524/SRX15206524.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206524/SRX15206524.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206524/SRX15206524.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206524/SRX15206524.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 14:47:15: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:47:15: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:47:18: 4000000 INFO @ Tue, 02 Aug 2022 14:47:23: 1000000 INFO @ Tue, 02 Aug 2022 14:47:26: 5000000 INFO @ Tue, 02 Aug 2022 14:47:32: 2000000 INFO @ Tue, 02 Aug 2022 14:47:34: 6000000 INFO @ Tue, 02 Aug 2022 14:47:40: 3000000 INFO @ Tue, 02 Aug 2022 14:47:41: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 14:47:41: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 14:47:41: #1 total tags in treatment: 6790887 INFO @ Tue, 02 Aug 2022 14:47:41: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:47:41: #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 14:47:41: #1 tags after filtering in treatment: 6790887 INFO @ Tue, 02 Aug 2022 14:47:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:47:41: #1 finished! INFO @ Tue, 02 Aug 2022 14:47:41: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:47:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:47:42: #2 number of paired peaks: 5849 INFO @ Tue, 02 Aug 2022 14:47:42: start model_add_line... INFO @ Tue, 02 Aug 2022 14:47:42: start X-correlation... INFO @ Tue, 02 Aug 2022 14:47:42: end of X-cor INFO @ Tue, 02 Aug 2022 14:47:42: #2 finished! INFO @ Tue, 02 Aug 2022 14:47:42: #2 predicted fragment length is 174 bps INFO @ Tue, 02 Aug 2022 14:47:42: #2 alternative fragment length(s) may be 174 bps INFO @ Tue, 02 Aug 2022 14:47:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206524/SRX15206524.05_model.r WARNING @ Tue, 02 Aug 2022 14:47:42: #2 Since the d (174) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:47:42: #2 You may need to consider one of the other alternative d(s): 174 WARNING @ Tue, 02 Aug 2022 14:47:42: #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 14:47:42: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:47:42: #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 14:47:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206524/SRX15206524.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206524/SRX15206524.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206524/SRX15206524.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206524/SRX15206524.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 14:47:45: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:47:45: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:47:48: 4000000 INFO @ Tue, 02 Aug 2022 14:47:54: 1000000 INFO @ Tue, 02 Aug 2022 14:47:56: 5000000 INFO @ Tue, 02 Aug 2022 14:48:02: 2000000 INFO @ Tue, 02 Aug 2022 14:48:03: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:48:04: 6000000 INFO @ Tue, 02 Aug 2022 14:48:10: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 14:48:10: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 14:48:10: #1 total tags in treatment: 6790887 INFO @ Tue, 02 Aug 2022 14:48:10: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:48:10: #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 14:48:10: 3000000 INFO @ Tue, 02 Aug 2022 14:48:10: #1 tags after filtering in treatment: 6790887 INFO @ Tue, 02 Aug 2022 14:48:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:48:10: #1 finished! INFO @ Tue, 02 Aug 2022 14:48:10: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:48:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:48:11: #2 number of paired peaks: 5849 INFO @ Tue, 02 Aug 2022 14:48:11: start model_add_line... INFO @ Tue, 02 Aug 2022 14:48:11: start X-correlation... INFO @ Tue, 02 Aug 2022 14:48:11: end of X-cor INFO @ Tue, 02 Aug 2022 14:48:11: #2 finished! INFO @ Tue, 02 Aug 2022 14:48:11: #2 predicted fragment length is 174 bps INFO @ Tue, 02 Aug 2022 14:48:11: #2 alternative fragment length(s) may be 174 bps INFO @ Tue, 02 Aug 2022 14:48:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206524/SRX15206524.10_model.r WARNING @ Tue, 02 Aug 2022 14:48:11: #2 Since the d (174) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:48:11: #2 You may need to consider one of the other alternative d(s): 174 WARNING @ Tue, 02 Aug 2022 14:48:11: #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 14:48:11: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:48:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:48:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206524/SRX15206524.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:48:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206524/SRX15206524.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:48:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206524/SRX15206524.05_summits.bed INFO @ Tue, 02 Aug 2022 14:48:13: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10188 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:48:18: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:48:25: 5000000 INFO @ Tue, 02 Aug 2022 14:48:32: 6000000 INFO @ Tue, 02 Aug 2022 14:48:32: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:48:37: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 14:48:37: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 14:48:37: #1 total tags in treatment: 6790887 INFO @ Tue, 02 Aug 2022 14:48:37: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:48:37: #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 14:48:37: #1 tags after filtering in treatment: 6790887 INFO @ Tue, 02 Aug 2022 14:48:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:48:37: #1 finished! INFO @ Tue, 02 Aug 2022 14:48:37: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:48:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:48:38: #2 number of paired peaks: 5849 INFO @ Tue, 02 Aug 2022 14:48:38: start model_add_line... INFO @ Tue, 02 Aug 2022 14:48:38: start X-correlation... INFO @ Tue, 02 Aug 2022 14:48:38: end of X-cor INFO @ Tue, 02 Aug 2022 14:48:38: #2 finished! INFO @ Tue, 02 Aug 2022 14:48:38: #2 predicted fragment length is 174 bps INFO @ Tue, 02 Aug 2022 14:48:38: #2 alternative fragment length(s) may be 174 bps INFO @ Tue, 02 Aug 2022 14:48:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206524/SRX15206524.20_model.r WARNING @ Tue, 02 Aug 2022 14:48:38: #2 Since the d (174) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:48:38: #2 You may need to consider one of the other alternative d(s): 174 WARNING @ Tue, 02 Aug 2022 14:48:38: #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 14:48:38: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:48:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:48:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206524/SRX15206524.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:48:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206524/SRX15206524.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:48:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206524/SRX15206524.10_summits.bed INFO @ Tue, 02 Aug 2022 14:48:41: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7429 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:48:59: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:49:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206524/SRX15206524.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:49:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206524/SRX15206524.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:49:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206524/SRX15206524.20_summits.bed INFO @ Tue, 02 Aug 2022 14:49:08: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4617 records, 4 fields): 20 millis CompletedMACS2peakCalling