Job ID = 16439007 SRX = SRX15206442 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:23:30 prefetch.2.10.7: 1) Downloading 'SRR19139368'... 2022-08-02T05:23:30 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:24:27 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:24:27 prefetch.2.10.7: 1) 'SRR19139368' was downloaded successfully 2022-08-02T05:24:27 prefetch.2.10.7: 'SRR19139368' has 0 unresolved dependencies Read 16395049 spots for SRR19139368/SRR19139368.sra Written 16395049 spots for SRR19139368/SRR19139368.sra 2022-08-02T05:25:58 prefetch.2.10.7: 1) Downloading 'SRR19139369'... 2022-08-02T05:25:58 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:26:51 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:26:51 prefetch.2.10.7: 1) 'SRR19139369' was downloaded successfully 2022-08-02T05:26:51 prefetch.2.10.7: 'SRR19139369' has 0 unresolved dependencies Read 16395049 spots for SRR19139369/SRR19139369.sra Written 16395049 spots for SRR19139369/SRR19139369.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439438 ("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: 00:39:24 32790098 reads; of these: 32790098 (100.00%) were unpaired; of these: 1943330 (5.93%) aligned 0 times 16078292 (49.03%) aligned exactly 1 time 14768476 (45.04%) aligned >1 times 94.07% overall alignment rate Time searching: 00:39:24 Overall time: 00:39:24 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 24 files... [bam_rmdupse_core] 21496462 / 30846768 = 0.6969 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 15:22:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206442/SRX15206442.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206442/SRX15206442.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206442/SRX15206442.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206442/SRX15206442.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 15:22:37: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:22:37: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:22:48: 1000000 INFO @ Tue, 02 Aug 2022 15:22:59: 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 15:23:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206442/SRX15206442.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206442/SRX15206442.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206442/SRX15206442.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206442/SRX15206442.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 15:23:06: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:23:06: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:23:10: 3000000 INFO @ Tue, 02 Aug 2022 15:23:16: 1000000 INFO @ Tue, 02 Aug 2022 15:23:20: 4000000 INFO @ Tue, 02 Aug 2022 15:23:26: 2000000 INFO @ Tue, 02 Aug 2022 15:23:32: 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 15:23:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206442/SRX15206442.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206442/SRX15206442.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206442/SRX15206442.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206442/SRX15206442.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 15:23:36: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:23:36: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:23:36: 3000000 INFO @ Tue, 02 Aug 2022 15:23:43: 6000000 INFO @ Tue, 02 Aug 2022 15:23:46: 4000000 INFO @ Tue, 02 Aug 2022 15:23:47: 1000000 INFO @ Tue, 02 Aug 2022 15:23:54: 7000000 INFO @ Tue, 02 Aug 2022 15:23:55: 5000000 INFO @ Tue, 02 Aug 2022 15:23:58: 2000000 INFO @ Tue, 02 Aug 2022 15:24:05: 8000000 INFO @ Tue, 02 Aug 2022 15:24:05: 6000000 INFO @ Tue, 02 Aug 2022 15:24:09: 3000000 INFO @ Tue, 02 Aug 2022 15:24:15: 7000000 INFO @ Tue, 02 Aug 2022 15:24:16: 9000000 INFO @ Tue, 02 Aug 2022 15:24:19: 4000000 INFO @ Tue, 02 Aug 2022 15:24:20: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 15:24:20: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 15:24:20: #1 total tags in treatment: 9350306 INFO @ Tue, 02 Aug 2022 15:24:20: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:24:20: #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 15:24:21: #1 tags after filtering in treatment: 9350306 INFO @ Tue, 02 Aug 2022 15:24:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:24:21: #1 finished! INFO @ Tue, 02 Aug 2022 15:24:21: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:24:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:24:22: #2 number of paired peaks: 6074 INFO @ Tue, 02 Aug 2022 15:24:22: start model_add_line... INFO @ Tue, 02 Aug 2022 15:24:22: start X-correlation... INFO @ Tue, 02 Aug 2022 15:24:22: end of X-cor INFO @ Tue, 02 Aug 2022 15:24:22: #2 finished! INFO @ Tue, 02 Aug 2022 15:24:22: #2 predicted fragment length is 168 bps INFO @ Tue, 02 Aug 2022 15:24:22: #2 alternative fragment length(s) may be 168 bps INFO @ Tue, 02 Aug 2022 15:24:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206442/SRX15206442.05_model.r WARNING @ Tue, 02 Aug 2022 15:24:22: #2 Since the d (168) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:24:22: #2 You may need to consider one of the other alternative d(s): 168 WARNING @ Tue, 02 Aug 2022 15:24:22: #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 15:24:22: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:24:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:24:25: 8000000 INFO @ Tue, 02 Aug 2022 15:24:30: 5000000 INFO @ Tue, 02 Aug 2022 15:24:35: 9000000 INFO @ Tue, 02 Aug 2022 15:24:38: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 15:24:38: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 15:24:38: #1 total tags in treatment: 9350306 INFO @ Tue, 02 Aug 2022 15:24:38: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:24:38: #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 15:24:38: #1 tags after filtering in treatment: 9350306 INFO @ Tue, 02 Aug 2022 15:24:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:24:38: #1 finished! INFO @ Tue, 02 Aug 2022 15:24:38: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:24:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:24:40: #2 number of paired peaks: 6074 INFO @ Tue, 02 Aug 2022 15:24:40: start model_add_line... INFO @ Tue, 02 Aug 2022 15:24:40: start X-correlation... INFO @ Tue, 02 Aug 2022 15:24:40: end of X-cor INFO @ Tue, 02 Aug 2022 15:24:40: #2 finished! INFO @ Tue, 02 Aug 2022 15:24:40: #2 predicted fragment length is 168 bps INFO @ Tue, 02 Aug 2022 15:24:40: #2 alternative fragment length(s) may be 168 bps INFO @ Tue, 02 Aug 2022 15:24:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206442/SRX15206442.10_model.r WARNING @ Tue, 02 Aug 2022 15:24:40: #2 Since the d (168) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:24:40: #2 You may need to consider one of the other alternative d(s): 168 WARNING @ Tue, 02 Aug 2022 15:24:40: #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 15:24:40: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:24:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:24:41: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:24:51: 7000000 INFO @ Tue, 02 Aug 2022 15:24:55: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:25:01: 8000000 INFO @ Tue, 02 Aug 2022 15:25:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206442/SRX15206442.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:25:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206442/SRX15206442.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:25:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206442/SRX15206442.05_summits.bed INFO @ Tue, 02 Aug 2022 15:25:07: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10131 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:25:11: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:25:12: 9000000 INFO @ Tue, 02 Aug 2022 15:25:15: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 15:25:15: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 15:25:15: #1 total tags in treatment: 9350306 INFO @ Tue, 02 Aug 2022 15:25:15: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:25:15: #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 15:25:16: #1 tags after filtering in treatment: 9350306 INFO @ Tue, 02 Aug 2022 15:25:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:25:16: #1 finished! INFO @ Tue, 02 Aug 2022 15:25:16: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:25:16: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:25:17: #2 number of paired peaks: 6074 INFO @ Tue, 02 Aug 2022 15:25:17: start model_add_line... INFO @ Tue, 02 Aug 2022 15:25:17: start X-correlation... INFO @ Tue, 02 Aug 2022 15:25:17: end of X-cor INFO @ Tue, 02 Aug 2022 15:25:17: #2 finished! INFO @ Tue, 02 Aug 2022 15:25:17: #2 predicted fragment length is 168 bps INFO @ Tue, 02 Aug 2022 15:25:17: #2 alternative fragment length(s) may be 168 bps INFO @ Tue, 02 Aug 2022 15:25:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206442/SRX15206442.20_model.r WARNING @ Tue, 02 Aug 2022 15:25:17: #2 Since the d (168) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:25:17: #2 You may need to consider one of the other alternative d(s): 168 WARNING @ Tue, 02 Aug 2022 15:25:17: #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 15:25:17: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:25:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:25:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206442/SRX15206442.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:25:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206442/SRX15206442.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:25:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206442/SRX15206442.10_summits.bed INFO @ Tue, 02 Aug 2022 15:25:22: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7113 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:25:49: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:26:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206442/SRX15206442.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:26:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206442/SRX15206442.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:26:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206442/SRX15206442.20_summits.bed INFO @ Tue, 02 Aug 2022 15:26:00: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4104 records, 4 fields): 15 millis CompletedMACS2peakCalling