Job ID = 16439176 SRX = SRX15206457 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:42:45 prefetch.2.10.7: 1) Downloading 'SRR19139349'... 2022-08-02T05:42:45 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:42:57 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:42:57 prefetch.2.10.7: 'SRR19139349' is valid 2022-08-02T05:42:57 prefetch.2.10.7: 1) 'SRR19139349' was downloaded successfully 2022-08-02T05:42:57 prefetch.2.10.7: 'SRR19139349' has 0 unresolved dependencies Read 7779277 spots for SRR19139349/SRR19139349.sra Written 7779277 spots for SRR19139349/SRR19139349.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439278 ("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: 00:02:50 7779277 reads; of these: 7779277 (100.00%) were unpaired; of these: 327265 (4.21%) aligned 0 times 4363414 (56.09%) aligned exactly 1 time 3088598 (39.70%) aligned >1 times 95.79% overall alignment rate Time searching: 00:02:50 Overall time: 00:02:50 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_rmdupse_core] 1250632 / 7452012 = 0.1678 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 14:49:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206457/SRX15206457.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206457/SRX15206457.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206457/SRX15206457.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206457/SRX15206457.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 14:49:03: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:49:03: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:49:13: 1000000 INFO @ Tue, 02 Aug 2022 14:49:23: 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 14:49:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206457/SRX15206457.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206457/SRX15206457.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206457/SRX15206457.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206457/SRX15206457.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 14:49:33: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:49:33: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:49:34: 3000000 INFO @ Tue, 02 Aug 2022 14:49:44: 1000000 INFO @ Tue, 02 Aug 2022 14:49:45: 4000000 INFO @ Tue, 02 Aug 2022 14:49:55: 2000000 INFO @ Tue, 02 Aug 2022 14:49:56: 5000000 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 14:50:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206457/SRX15206457.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206457/SRX15206457.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206457/SRX15206457.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206457/SRX15206457.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 14:50:03: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:50:03: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:50:06: 3000000 INFO @ Tue, 02 Aug 2022 14:50:08: 6000000 INFO @ Tue, 02 Aug 2022 14:50:10: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:50:11: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:50:11: #1 total tags in treatment: 6201380 INFO @ Tue, 02 Aug 2022 14:50:11: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:50:11: #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 14:50:11: #1 tags after filtering in treatment: 6201380 INFO @ Tue, 02 Aug 2022 14:50:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:50:11: #1 finished! INFO @ Tue, 02 Aug 2022 14:50:11: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:50:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:50:11: #2 number of paired peaks: 1983 INFO @ Tue, 02 Aug 2022 14:50:11: start model_add_line... INFO @ Tue, 02 Aug 2022 14:50:11: start X-correlation... INFO @ Tue, 02 Aug 2022 14:50:12: end of X-cor INFO @ Tue, 02 Aug 2022 14:50:12: #2 finished! INFO @ Tue, 02 Aug 2022 14:50:12: #2 predicted fragment length is 99 bps INFO @ Tue, 02 Aug 2022 14:50:12: #2 alternative fragment length(s) may be 99 bps INFO @ Tue, 02 Aug 2022 14:50:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206457/SRX15206457.05_model.r WARNING @ Tue, 02 Aug 2022 14:50:12: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:50:12: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Tue, 02 Aug 2022 14:50:12: #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 14:50:12: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:50:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:50:16: 1000000 INFO @ Tue, 02 Aug 2022 14:50:18: 4000000 INFO @ Tue, 02 Aug 2022 14:50:26: 2000000 INFO @ Tue, 02 Aug 2022 14:50:28: 5000000 INFO @ Tue, 02 Aug 2022 14:50:32: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:50:37: 3000000 INFO @ Tue, 02 Aug 2022 14:50:39: 6000000 INFO @ Tue, 02 Aug 2022 14:50:41: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:50:41: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:50:41: #1 total tags in treatment: 6201380 INFO @ Tue, 02 Aug 2022 14:50:41: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:50:41: #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 14:50:41: #1 tags after filtering in treatment: 6201380 INFO @ Tue, 02 Aug 2022 14:50:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:50:41: #1 finished! INFO @ Tue, 02 Aug 2022 14:50:41: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:50:41: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:50:42: #2 number of paired peaks: 1983 INFO @ Tue, 02 Aug 2022 14:50:42: start model_add_line... INFO @ Tue, 02 Aug 2022 14:50:42: start X-correlation... INFO @ Tue, 02 Aug 2022 14:50:42: end of X-cor INFO @ Tue, 02 Aug 2022 14:50:42: #2 finished! INFO @ Tue, 02 Aug 2022 14:50:42: #2 predicted fragment length is 99 bps INFO @ Tue, 02 Aug 2022 14:50:42: #2 alternative fragment length(s) may be 99 bps INFO @ Tue, 02 Aug 2022 14:50:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206457/SRX15206457.10_model.r WARNING @ Tue, 02 Aug 2022 14:50:42: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:50:42: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Tue, 02 Aug 2022 14:50:42: #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 14:50:42: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:50:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:50:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206457/SRX15206457.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:50:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206457/SRX15206457.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:50:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206457/SRX15206457.05_summits.bed INFO @ Tue, 02 Aug 2022 14:50:43: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (4015 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:50:47: 4000000 INFO @ Tue, 02 Aug 2022 14:50:56: 5000000 INFO @ Tue, 02 Aug 2022 14:51:02: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:51:06: 6000000 INFO @ Tue, 02 Aug 2022 14:51:07: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:51:07: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:51:07: #1 total tags in treatment: 6201380 INFO @ Tue, 02 Aug 2022 14:51:07: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:51:07: #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 14:51:07: #1 tags after filtering in treatment: 6201380 INFO @ Tue, 02 Aug 2022 14:51:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:51:08: #1 finished! INFO @ Tue, 02 Aug 2022 14:51:08: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:51:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:51:08: #2 number of paired peaks: 1983 INFO @ Tue, 02 Aug 2022 14:51:08: start model_add_line... INFO @ Tue, 02 Aug 2022 14:51:08: start X-correlation... INFO @ Tue, 02 Aug 2022 14:51:08: end of X-cor INFO @ Tue, 02 Aug 2022 14:51:08: #2 finished! INFO @ Tue, 02 Aug 2022 14:51:08: #2 predicted fragment length is 99 bps INFO @ Tue, 02 Aug 2022 14:51:08: #2 alternative fragment length(s) may be 99 bps INFO @ Tue, 02 Aug 2022 14:51:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206457/SRX15206457.20_model.r WARNING @ Tue, 02 Aug 2022 14:51:08: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:51:08: #2 You may need to consider one of the other alternative d(s): 99 WARNING @ Tue, 02 Aug 2022 14:51:08: #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 14:51:08: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:51:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:51:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206457/SRX15206457.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:51:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206457/SRX15206457.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:51:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206457/SRX15206457.10_summits.bed INFO @ Tue, 02 Aug 2022 14:51:13: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1914 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:51:29: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:51:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206457/SRX15206457.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:51:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206457/SRX15206457.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:51:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206457/SRX15206457.20_summits.bed INFO @ Tue, 02 Aug 2022 14:51:40: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (877 records, 4 fields): 25 millis CompletedMACS2peakCalling