Job ID = 16440251 SRX = SRX15369009 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T08:36:26 prefetch.2.10.7: 1) Downloading 'SRR19308738'... 2022-08-02T08:36:26 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T08:37:00 prefetch.2.10.7: HTTPS download succeed 2022-08-02T08:37:01 prefetch.2.10.7: 'SRR19308738' is valid 2022-08-02T08:37:01 prefetch.2.10.7: 1) 'SRR19308738' was downloaded successfully 2022-08-02T08:37:01 prefetch.2.10.7: 'SRR19308738' has 0 unresolved dependencies Read 16247852 spots for SRR19308738/SRR19308738.sra Written 16247852 spots for SRR19308738/SRR19308738.sra fastq に変換しました。 bowtie でマッピング中... Your job 16440825 ("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: 00:14:54 16247852 reads; of these: 16247852 (100.00%) were unpaired; of these: 719025 (4.43%) aligned 0 times 10463788 (64.40%) aligned exactly 1 time 5065039 (31.17%) aligned >1 times 95.57% overall alignment rate Time searching: 00:14:54 Overall time: 00:14:54 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] 13070835 / 15528827 = 0.8417 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 17:57:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15369009/SRX15369009.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15369009/SRX15369009.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15369009/SRX15369009.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15369009/SRX15369009.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 17:57:47: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:57:47: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:58:02: 1000000 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 17:58:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15369009/SRX15369009.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15369009/SRX15369009.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15369009/SRX15369009.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15369009/SRX15369009.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 17:58:15: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:58:15: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:58:16: 2000000 INFO @ Tue, 02 Aug 2022 17:58:22: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 17:58:22: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 17:58:22: #1 total tags in treatment: 2457992 INFO @ Tue, 02 Aug 2022 17:58:22: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:58:22: #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 17:58:22: #1 tags after filtering in treatment: 2457992 INFO @ Tue, 02 Aug 2022 17:58:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 17:58:22: #1 finished! INFO @ Tue, 02 Aug 2022 17:58:22: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:58:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:58:23: #2 number of paired peaks: 4600 INFO @ Tue, 02 Aug 2022 17:58:23: start model_add_line... INFO @ Tue, 02 Aug 2022 17:58:23: start X-correlation... INFO @ Tue, 02 Aug 2022 17:58:23: end of X-cor INFO @ Tue, 02 Aug 2022 17:58:23: #2 finished! INFO @ Tue, 02 Aug 2022 17:58:23: #2 predicted fragment length is 82 bps INFO @ Tue, 02 Aug 2022 17:58:23: #2 alternative fragment length(s) may be 82 bps INFO @ Tue, 02 Aug 2022 17:58:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15369009/SRX15369009.05_model.r WARNING @ Tue, 02 Aug 2022 17:58:23: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:58:23: #2 You may need to consider one of the other alternative d(s): 82 WARNING @ Tue, 02 Aug 2022 17:58:23: #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 17:58:23: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:58:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:58:29: 1000000 INFO @ Tue, 02 Aug 2022 17:58:32: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:58:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15369009/SRX15369009.05_peaks.xls INFO @ Tue, 02 Aug 2022 17:58:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15369009/SRX15369009.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:58:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15369009/SRX15369009.05_summits.bed INFO @ Tue, 02 Aug 2022 17:58:37: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4974 records, 4 fields): 64 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 17:58:43: 2000000 INFO @ Tue, 02 Aug 2022 17:58:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15369009/SRX15369009.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15369009/SRX15369009.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15369009/SRX15369009.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15369009/SRX15369009.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 17:58:46: #1 read tag files... INFO @ Tue, 02 Aug 2022 17:58:46: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 17:58:49: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 17:58:49: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 17:58:49: #1 total tags in treatment: 2457992 INFO @ Tue, 02 Aug 2022 17:58:49: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:58:49: #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 17:58:49: #1 tags after filtering in treatment: 2457992 INFO @ Tue, 02 Aug 2022 17:58:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 17:58:49: #1 finished! INFO @ Tue, 02 Aug 2022 17:58:49: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:58:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:58:49: #2 number of paired peaks: 4600 INFO @ Tue, 02 Aug 2022 17:58:49: start model_add_line... INFO @ Tue, 02 Aug 2022 17:58:50: start X-correlation... INFO @ Tue, 02 Aug 2022 17:58:50: end of X-cor INFO @ Tue, 02 Aug 2022 17:58:50: #2 finished! INFO @ Tue, 02 Aug 2022 17:58:50: #2 predicted fragment length is 82 bps INFO @ Tue, 02 Aug 2022 17:58:50: #2 alternative fragment length(s) may be 82 bps INFO @ Tue, 02 Aug 2022 17:58:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15369009/SRX15369009.10_model.r WARNING @ Tue, 02 Aug 2022 17:58:50: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:58:50: #2 You may need to consider one of the other alternative d(s): 82 WARNING @ Tue, 02 Aug 2022 17:58:50: #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 17:58:50: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:58:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:58:58: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:59:00: 1000000 INFO @ Tue, 02 Aug 2022 17:59:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15369009/SRX15369009.10_peaks.xls BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 17:59:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15369009/SRX15369009.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:59:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15369009/SRX15369009.10_summits.bed INFO @ Tue, 02 Aug 2022 17:59:04: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1928 records, 4 fields): 46 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 17:59:14: 2000000 INFO @ Tue, 02 Aug 2022 17:59:20: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 17:59:20: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 17:59:20: #1 total tags in treatment: 2457992 INFO @ Tue, 02 Aug 2022 17:59:20: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 17:59:20: #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 17:59:20: #1 tags after filtering in treatment: 2457992 INFO @ Tue, 02 Aug 2022 17:59:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 17:59:20: #1 finished! INFO @ Tue, 02 Aug 2022 17:59:20: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 17:59:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 17:59:21: #2 number of paired peaks: 4600 INFO @ Tue, 02 Aug 2022 17:59:21: start model_add_line... INFO @ Tue, 02 Aug 2022 17:59:21: start X-correlation... INFO @ Tue, 02 Aug 2022 17:59:21: end of X-cor INFO @ Tue, 02 Aug 2022 17:59:21: #2 finished! INFO @ Tue, 02 Aug 2022 17:59:21: #2 predicted fragment length is 82 bps INFO @ Tue, 02 Aug 2022 17:59:21: #2 alternative fragment length(s) may be 82 bps INFO @ Tue, 02 Aug 2022 17:59:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15369009/SRX15369009.20_model.r WARNING @ Tue, 02 Aug 2022 17:59:21: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 17:59:21: #2 You may need to consider one of the other alternative d(s): 82 WARNING @ Tue, 02 Aug 2022 17:59:21: #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 17:59:21: #3 Call peaks... INFO @ Tue, 02 Aug 2022 17:59:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 17:59:30: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 17:59:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15369009/SRX15369009.20_peaks.xls INFO @ Tue, 02 Aug 2022 17:59:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15369009/SRX15369009.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 17:59:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15369009/SRX15369009.20_summits.bed INFO @ Tue, 02 Aug 2022 17:59:35: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (524 records, 4 fields): 77 millis CompletedMACS2peakCalling