Job ID = 16438979 SRX = SRX15206531 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:18:54 prefetch.2.10.7: 1) Downloading 'SRR19139261'... 2022-08-02T05:18:54 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:20:15 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:20:15 prefetch.2.10.7: 1) 'SRR19139261' was downloaded successfully 2022-08-02T05:20:16 prefetch.2.10.7: 'SRR19139261' has 0 unresolved dependencies Read 19333458 spots for SRR19139261/SRR19139261.sra Written 19333458 spots for SRR19139261/SRR19139261.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439167 ("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: 00:16:36 19333458 reads; of these: 19333458 (100.00%) were unpaired; of these: 1528978 (7.91%) aligned 0 times 10637659 (55.02%) aligned exactly 1 time 7166821 (37.07%) aligned >1 times 92.09% overall alignment rate Time searching: 00:16:36 Overall time: 00:16:36 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 16 files... [bam_rmdupse_core] 10046169 / 17804480 = 0.5642 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 14:46:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206531/SRX15206531.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206531/SRX15206531.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206531/SRX15206531.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206531/SRX15206531.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 14:46:18: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:46:18: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:46:27: 1000000 INFO @ Tue, 02 Aug 2022 14:46:37: 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 14:46:46: 3000000 INFO @ Tue, 02 Aug 2022 14:46:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206531/SRX15206531.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206531/SRX15206531.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206531/SRX15206531.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206531/SRX15206531.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 14:46:48: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:46:48: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:46:57: 4000000 INFO @ Tue, 02 Aug 2022 14:46:59: 1000000 INFO @ Tue, 02 Aug 2022 14:47:08: 5000000 INFO @ Tue, 02 Aug 2022 14:47:10: 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 14:47:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206531/SRX15206531.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206531/SRX15206531.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206531/SRX15206531.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206531/SRX15206531.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 14:47:18: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:47:18: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:47:18: 6000000 INFO @ Tue, 02 Aug 2022 14:47:21: 3000000 INFO @ Tue, 02 Aug 2022 14:47:29: 1000000 INFO @ Tue, 02 Aug 2022 14:47:29: 7000000 INFO @ Tue, 02 Aug 2022 14:47:32: 4000000 INFO @ Tue, 02 Aug 2022 14:47:37: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 14:47:37: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 14:47:37: #1 total tags in treatment: 7758311 INFO @ Tue, 02 Aug 2022 14:47:37: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:47:37: #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 14:47:37: #1 tags after filtering in treatment: 7758311 INFO @ Tue, 02 Aug 2022 14:47:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:47:37: #1 finished! INFO @ Tue, 02 Aug 2022 14:47:37: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:47:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:47:38: #2 number of paired peaks: 3677 INFO @ Tue, 02 Aug 2022 14:47:38: start model_add_line... INFO @ Tue, 02 Aug 2022 14:47:38: start X-correlation... INFO @ Tue, 02 Aug 2022 14:47:38: end of X-cor INFO @ Tue, 02 Aug 2022 14:47:38: #2 finished! INFO @ Tue, 02 Aug 2022 14:47:38: #2 predicted fragment length is 173 bps INFO @ Tue, 02 Aug 2022 14:47:38: #2 alternative fragment length(s) may be 173 bps INFO @ Tue, 02 Aug 2022 14:47:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206531/SRX15206531.05_model.r WARNING @ Tue, 02 Aug 2022 14:47:38: #2 Since the d (173) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:47:38: #2 You may need to consider one of the other alternative d(s): 173 WARNING @ Tue, 02 Aug 2022 14:47:38: #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 14:47:38: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:47:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:47:39: 2000000 INFO @ Tue, 02 Aug 2022 14:47:42: 5000000 INFO @ Tue, 02 Aug 2022 14:47:50: 3000000 INFO @ Tue, 02 Aug 2022 14:47:52: 6000000 INFO @ Tue, 02 Aug 2022 14:48:00: 4000000 INFO @ Tue, 02 Aug 2022 14:48:01: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:48:03: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:48:10: 5000000 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: 7758311 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: #1 tags after filtering in treatment: 7758311 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: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206531/SRX15206531.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:48:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206531/SRX15206531.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:48:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206531/SRX15206531.05_summits.bed INFO @ Tue, 02 Aug 2022 14:48:11: #2 number of paired peaks: 3677 INFO @ Tue, 02 Aug 2022 14:48:11: start model_add_line... INFO @ Tue, 02 Aug 2022 14:48:11: Done! 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 173 bps INFO @ Tue, 02 Aug 2022 14:48:11: #2 alternative fragment length(s) may be 173 bps INFO @ Tue, 02 Aug 2022 14:48:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206531/SRX15206531.10_model.r WARNING @ Tue, 02 Aug 2022 14:48:11: #2 Since the d (173) 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): 173 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... pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (8195 records, 4 fields): 47 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:48:19: 6000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:48:28: 7000000 INFO @ Tue, 02 Aug 2022 14:48:33: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:48:34: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 14:48:34: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 14:48:34: #1 total tags in treatment: 7758311 INFO @ Tue, 02 Aug 2022 14:48:34: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:48:34: #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 14:48:35: #1 tags after filtering in treatment: 7758311 INFO @ Tue, 02 Aug 2022 14:48:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:48:35: #1 finished! INFO @ Tue, 02 Aug 2022 14:48:35: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:48:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:48:35: #2 number of paired peaks: 3677 INFO @ Tue, 02 Aug 2022 14:48:35: start model_add_line... INFO @ Tue, 02 Aug 2022 14:48:35: start X-correlation... INFO @ Tue, 02 Aug 2022 14:48:35: end of X-cor INFO @ Tue, 02 Aug 2022 14:48:35: #2 finished! INFO @ Tue, 02 Aug 2022 14:48:35: #2 predicted fragment length is 173 bps INFO @ Tue, 02 Aug 2022 14:48:35: #2 alternative fragment length(s) may be 173 bps INFO @ Tue, 02 Aug 2022 14:48:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206531/SRX15206531.20_model.r WARNING @ Tue, 02 Aug 2022 14:48:35: #2 Since the d (173) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:48:35: #2 You may need to consider one of the other alternative d(s): 173 WARNING @ Tue, 02 Aug 2022 14:48:35: #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 14:48:35: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:48:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:48:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206531/SRX15206531.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:48:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206531/SRX15206531.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:48:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206531/SRX15206531.10_summits.bed INFO @ Tue, 02 Aug 2022 14:48:43: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5038 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:48:58: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:49:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206531/SRX15206531.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:49:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206531/SRX15206531.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:49:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206531/SRX15206531.20_summits.bed INFO @ Tue, 02 Aug 2022 14:49:07: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2919 records, 4 fields): 28 millis CompletedMACS2peakCalling