Job ID = 16438923 SRX = SRX15206519 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:10:10 prefetch.2.10.7: 1) Downloading 'SRR19139273'... 2022-08-02T05:10:10 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:10:34 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:10:34 prefetch.2.10.7: 'SRR19139273' is valid 2022-08-02T05:10:34 prefetch.2.10.7: 1) 'SRR19139273' was downloaded successfully 2022-08-02T05:10:34 prefetch.2.10.7: 'SRR19139273' has 0 unresolved dependencies Read 12607827 spots for SRR19139273/SRR19139273.sra Written 12607827 spots for SRR19139273/SRR19139273.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438981 ("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: 00:06:03 12607827 reads; of these: 12607827 (100.00%) were unpaired; of these: 618976 (4.91%) aligned 0 times 8390454 (66.55%) aligned exactly 1 time 3598397 (28.54%) aligned >1 times 95.09% overall alignment rate Time searching: 00:06:03 Overall time: 00:06:03 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 8 files... [bam_rmdupse_core] 8643829 / 11988851 = 0.7210 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 14:19:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206519/SRX15206519.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206519/SRX15206519.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206519/SRX15206519.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206519/SRX15206519.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 14:19:52: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:19:52: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:19:59: 1000000 INFO @ Tue, 02 Aug 2022 14:20:05: 2000000 INFO @ Tue, 02 Aug 2022 14:20:11: 3000000 INFO @ Tue, 02 Aug 2022 14:20:14: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 14:20:14: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 14:20:14: #1 total tags in treatment: 3345022 INFO @ Tue, 02 Aug 2022 14:20:14: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:20:14: #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 14:20:14: #1 tags after filtering in treatment: 3345022 INFO @ Tue, 02 Aug 2022 14:20:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:20:14: #1 finished! INFO @ Tue, 02 Aug 2022 14:20:14: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:20:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:20:14: #2 number of paired peaks: 4698 INFO @ Tue, 02 Aug 2022 14:20:14: start model_add_line... INFO @ Tue, 02 Aug 2022 14:20:14: start X-correlation... INFO @ Tue, 02 Aug 2022 14:20:14: end of X-cor INFO @ Tue, 02 Aug 2022 14:20:14: #2 finished! INFO @ Tue, 02 Aug 2022 14:20:14: #2 predicted fragment length is 161 bps INFO @ Tue, 02 Aug 2022 14:20:14: #2 alternative fragment length(s) may be 161 bps INFO @ Tue, 02 Aug 2022 14:20:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206519/SRX15206519.05_model.r WARNING @ Tue, 02 Aug 2022 14:20:14: #2 Since the d (161) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:20:14: #2 You may need to consider one of the other alternative d(s): 161 WARNING @ Tue, 02 Aug 2022 14:20:14: #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 14:20:14: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:20:14: #3 Pre-compute pvalue-qvalue table... 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 14:20:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206519/SRX15206519.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206519/SRX15206519.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206519/SRX15206519.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206519/SRX15206519.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 14:20:22: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:20:22: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:20:22: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:20:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206519/SRX15206519.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:20:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206519/SRX15206519.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:20:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206519/SRX15206519.05_summits.bed INFO @ Tue, 02 Aug 2022 14:20:26: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7239 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:20:29: 1000000 INFO @ Tue, 02 Aug 2022 14:20:35: 2000000 INFO @ Tue, 02 Aug 2022 14:20:41: 3000000 INFO @ Tue, 02 Aug 2022 14:20:43: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 14:20:43: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 14:20:43: #1 total tags in treatment: 3345022 INFO @ Tue, 02 Aug 2022 14:20:43: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:20:43: #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 14:20:43: #1 tags after filtering in treatment: 3345022 INFO @ Tue, 02 Aug 2022 14:20:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:20:43: #1 finished! INFO @ Tue, 02 Aug 2022 14:20:43: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:20:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:20:44: #2 number of paired peaks: 4698 INFO @ Tue, 02 Aug 2022 14:20:44: start model_add_line... INFO @ Tue, 02 Aug 2022 14:20:44: start X-correlation... INFO @ Tue, 02 Aug 2022 14:20:44: end of X-cor INFO @ Tue, 02 Aug 2022 14:20:44: #2 finished! INFO @ Tue, 02 Aug 2022 14:20:44: #2 predicted fragment length is 161 bps INFO @ Tue, 02 Aug 2022 14:20:44: #2 alternative fragment length(s) may be 161 bps INFO @ Tue, 02 Aug 2022 14:20:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206519/SRX15206519.10_model.r WARNING @ Tue, 02 Aug 2022 14:20:44: #2 Since the d (161) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:20:44: #2 You may need to consider one of the other alternative d(s): 161 WARNING @ Tue, 02 Aug 2022 14:20:44: #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 14:20:44: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:20:44: #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 14:20:52: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:20:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206519/SRX15206519.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206519/SRX15206519.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206519/SRX15206519.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206519/SRX15206519.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 14:20:52: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:20:52: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:20:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206519/SRX15206519.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:20:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206519/SRX15206519.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:20:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206519/SRX15206519.10_summits.bed INFO @ Tue, 02 Aug 2022 14:20:56: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4619 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:21:00: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:21:08: 2000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:21:16: 3000000 INFO @ Tue, 02 Aug 2022 14:21:18: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 14:21:18: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 14:21:18: #1 total tags in treatment: 3345022 INFO @ Tue, 02 Aug 2022 14:21:18: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:21:18: #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 14:21:18: #1 tags after filtering in treatment: 3345022 INFO @ Tue, 02 Aug 2022 14:21:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:21:18: #1 finished! INFO @ Tue, 02 Aug 2022 14:21:18: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:21:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:21:19: #2 number of paired peaks: 4698 INFO @ Tue, 02 Aug 2022 14:21:19: start model_add_line... INFO @ Tue, 02 Aug 2022 14:21:19: start X-correlation... INFO @ Tue, 02 Aug 2022 14:21:19: end of X-cor INFO @ Tue, 02 Aug 2022 14:21:19: #2 finished! INFO @ Tue, 02 Aug 2022 14:21:19: #2 predicted fragment length is 161 bps INFO @ Tue, 02 Aug 2022 14:21:19: #2 alternative fragment length(s) may be 161 bps INFO @ Tue, 02 Aug 2022 14:21:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206519/SRX15206519.20_model.r WARNING @ Tue, 02 Aug 2022 14:21:19: #2 Since the d (161) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:21:19: #2 You may need to consider one of the other alternative d(s): 161 WARNING @ Tue, 02 Aug 2022 14:21:19: #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 14:21:19: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:21:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:21:27: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:21:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206519/SRX15206519.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:21:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206519/SRX15206519.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:21:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206519/SRX15206519.20_summits.bed INFO @ Tue, 02 Aug 2022 14:21:31: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2460 records, 4 fields): 42 millis CompletedMACS2peakCalling