Job ID = 16439318 SRX = SRX15206496 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:53:05 prefetch.2.10.7: 1) Downloading 'SRR19139297'... 2022-08-02T05:53:05 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:53:18 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:53:18 prefetch.2.10.7: 'SRR19139297' is valid 2022-08-02T05:53:18 prefetch.2.10.7: 1) 'SRR19139297' was downloaded successfully 2022-08-02T05:53:18 prefetch.2.10.7: 'SRR19139297' has 0 unresolved dependencies Read 6009666 spots for SRR19139297/SRR19139297.sra Written 6009666 spots for SRR19139297/SRR19139297.sra 2022-08-02T05:53:50 prefetch.2.10.7: 1) Downloading 'SRR19139298'... 2022-08-02T05:53:50 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:54:04 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:54:04 prefetch.2.10.7: 'SRR19139298' is valid 2022-08-02T05:54:04 prefetch.2.10.7: 1) 'SRR19139298' was downloaded successfully 2022-08-02T05:54:04 prefetch.2.10.7: 'SRR19139298' has 0 unresolved dependencies Read 6009666 spots for SRR19139298/SRR19139298.sra Written 6009666 spots for SRR19139298/SRR19139298.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439403 ("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: 00:07:25 12019332 reads; of these: 12019332 (100.00%) were unpaired; of these: 431003 (3.59%) aligned 0 times 6275532 (52.21%) aligned exactly 1 time 5312797 (44.20%) aligned >1 times 96.41% overall alignment rate Time searching: 00:07:25 Overall time: 00:07:25 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] 2074300 / 11588329 = 0.1790 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 15:06:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206496/SRX15206496.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206496/SRX15206496.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206496/SRX15206496.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206496/SRX15206496.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 15:06:41: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:06:41: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:06:53: 1000000 INFO @ Tue, 02 Aug 2022 15:07:05: 2000000 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 15:07:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206496/SRX15206496.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206496/SRX15206496.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206496/SRX15206496.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206496/SRX15206496.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 15:07:11: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:07:11: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:07:18: 3000000 INFO @ Tue, 02 Aug 2022 15:07:22: 1000000 INFO @ Tue, 02 Aug 2022 15:07:32: 4000000 INFO @ Tue, 02 Aug 2022 15:07:32: 2000000 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 15:07:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206496/SRX15206496.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206496/SRX15206496.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206496/SRX15206496.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206496/SRX15206496.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 15:07:41: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:07:41: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:07:43: 3000000 INFO @ Tue, 02 Aug 2022 15:07:45: 5000000 INFO @ Tue, 02 Aug 2022 15:07:51: 1000000 INFO @ Tue, 02 Aug 2022 15:07:53: 4000000 INFO @ Tue, 02 Aug 2022 15:08:00: 6000000 INFO @ Tue, 02 Aug 2022 15:08:01: 2000000 INFO @ Tue, 02 Aug 2022 15:08:03: 5000000 INFO @ Tue, 02 Aug 2022 15:08:09: 3000000 INFO @ Tue, 02 Aug 2022 15:08:13: 7000000 INFO @ Tue, 02 Aug 2022 15:08:14: 6000000 INFO @ Tue, 02 Aug 2022 15:08:18: 4000000 INFO @ Tue, 02 Aug 2022 15:08:24: 7000000 INFO @ Tue, 02 Aug 2022 15:08:26: 8000000 INFO @ Tue, 02 Aug 2022 15:08:27: 5000000 INFO @ Tue, 02 Aug 2022 15:08:35: 8000000 INFO @ Tue, 02 Aug 2022 15:08:36: 6000000 INFO @ Tue, 02 Aug 2022 15:08:38: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:08:45: 7000000 INFO @ Tue, 02 Aug 2022 15:08:45: 9000000 INFO @ Tue, 02 Aug 2022 15:08:46: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:08:46: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:08:46: #1 total tags in treatment: 9514029 INFO @ Tue, 02 Aug 2022 15:08:46: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:08:46: #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 15:08:46: #1 tags after filtering in treatment: 9514029 INFO @ Tue, 02 Aug 2022 15:08:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:08:46: #1 finished! INFO @ Tue, 02 Aug 2022 15:08:46: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:08:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:08:47: #2 number of paired peaks: 3678 INFO @ Tue, 02 Aug 2022 15:08:47: start model_add_line... INFO @ Tue, 02 Aug 2022 15:08:47: start X-correlation... INFO @ Tue, 02 Aug 2022 15:08:47: end of X-cor INFO @ Tue, 02 Aug 2022 15:08:47: #2 finished! INFO @ Tue, 02 Aug 2022 15:08:47: #2 predicted fragment length is 132 bps INFO @ Tue, 02 Aug 2022 15:08:47: #2 alternative fragment length(s) may be 132 bps INFO @ Tue, 02 Aug 2022 15:08:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206496/SRX15206496.05_model.r WARNING @ Tue, 02 Aug 2022 15:08:47: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:08:47: #2 You may need to consider one of the other alternative d(s): 132 WARNING @ Tue, 02 Aug 2022 15:08:47: #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 15:08:47: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:08:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:08:50: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:08:50: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:08:50: #1 total tags in treatment: 9514029 INFO @ Tue, 02 Aug 2022 15:08:50: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:08:50: #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 15:08:51: #1 tags after filtering in treatment: 9514029 INFO @ Tue, 02 Aug 2022 15:08:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:08:51: #1 finished! INFO @ Tue, 02 Aug 2022 15:08:51: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:08:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:08:52: #2 number of paired peaks: 3678 INFO @ Tue, 02 Aug 2022 15:08:52: start model_add_line... INFO @ Tue, 02 Aug 2022 15:08:52: start X-correlation... INFO @ Tue, 02 Aug 2022 15:08:52: end of X-cor INFO @ Tue, 02 Aug 2022 15:08:52: #2 finished! INFO @ Tue, 02 Aug 2022 15:08:52: #2 predicted fragment length is 132 bps INFO @ Tue, 02 Aug 2022 15:08:52: #2 alternative fragment length(s) may be 132 bps INFO @ Tue, 02 Aug 2022 15:08:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206496/SRX15206496.10_model.r WARNING @ Tue, 02 Aug 2022 15:08:52: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:08:52: #2 You may need to consider one of the other alternative d(s): 132 WARNING @ Tue, 02 Aug 2022 15:08:52: #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 15:08:52: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:08:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:08:55: 8000000 INFO @ Tue, 02 Aug 2022 15:09:04: 9000000 INFO @ Tue, 02 Aug 2022 15:09:08: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:09:08: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:09:08: #1 total tags in treatment: 9514029 INFO @ Tue, 02 Aug 2022 15:09:08: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:09:08: #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 15:09:08: #1 tags after filtering in treatment: 9514029 INFO @ Tue, 02 Aug 2022 15:09:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:09:08: #1 finished! INFO @ Tue, 02 Aug 2022 15:09:08: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:09:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:09:09: #2 number of paired peaks: 3678 INFO @ Tue, 02 Aug 2022 15:09:09: start model_add_line... INFO @ Tue, 02 Aug 2022 15:09:10: start X-correlation... INFO @ Tue, 02 Aug 2022 15:09:10: end of X-cor INFO @ Tue, 02 Aug 2022 15:09:10: #2 finished! INFO @ Tue, 02 Aug 2022 15:09:10: #2 predicted fragment length is 132 bps INFO @ Tue, 02 Aug 2022 15:09:10: #2 alternative fragment length(s) may be 132 bps INFO @ Tue, 02 Aug 2022 15:09:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206496/SRX15206496.20_model.r WARNING @ Tue, 02 Aug 2022 15:09:10: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:09:10: #2 You may need to consider one of the other alternative d(s): 132 WARNING @ Tue, 02 Aug 2022 15:09:10: #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 15:09:10: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:09:10: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:09:21: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:09:27: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:09:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206496/SRX15206496.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:09:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206496/SRX15206496.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:09:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206496/SRX15206496.05_summits.bed INFO @ Tue, 02 Aug 2022 15:09:39: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (7872 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:09:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206496/SRX15206496.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:09:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206496/SRX15206496.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:09:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206496/SRX15206496.10_summits.bed INFO @ Tue, 02 Aug 2022 15:09:43: Done! INFO @ Tue, 02 Aug 2022 15:09:43: #3 Call peaks for each chromosome... pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4762 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:09:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206496/SRX15206496.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:09:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206496/SRX15206496.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:09:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206496/SRX15206496.20_summits.bed INFO @ Tue, 02 Aug 2022 15:09:59: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2400 records, 4 fields): 24 millis CompletedMACS2peakCalling