Job ID = 16438693 SRX = SRX15206506 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:05:11 prefetch.2.10.7: 1) Downloading 'SRR19139286'... 2022-08-02T05:05:11 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:05:47 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:05:48 prefetch.2.10.7: 'SRR19139286' is valid 2022-08-02T05:05:48 prefetch.2.10.7: 1) 'SRR19139286' was downloaded successfully 2022-08-02T05:05:48 prefetch.2.10.7: 'SRR19139286' has 0 unresolved dependencies Read 20340984 spots for SRR19139286/SRR19139286.sra Written 20340984 spots for SRR19139286/SRR19139286.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438966 ("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: 00:06:58 20340984 reads; of these: 20340984 (100.00%) were unpaired; of these: 914169 (4.49%) aligned 0 times 15066744 (74.07%) aligned exactly 1 time 4360071 (21.43%) aligned >1 times 95.51% overall alignment rate Time searching: 00:06:58 Overall time: 00:06:58 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] 8743659 / 19426815 = 0.4501 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 14:17:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206506/SRX15206506.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206506/SRX15206506.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206506/SRX15206506.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206506/SRX15206506.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 14:17:53: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:17:53: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:17:59: 1000000 INFO @ Tue, 02 Aug 2022 14:18:05: 2000000 INFO @ Tue, 02 Aug 2022 14:18:11: 3000000 INFO @ Tue, 02 Aug 2022 14:18:16: 4000000 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 14:18:22: 5000000 INFO @ Tue, 02 Aug 2022 14:18:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206506/SRX15206506.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206506/SRX15206506.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206506/SRX15206506.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206506/SRX15206506.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 14:18:23: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:18:23: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:18:28: 6000000 INFO @ Tue, 02 Aug 2022 14:18:30: 1000000 INFO @ Tue, 02 Aug 2022 14:18:33: 7000000 INFO @ Tue, 02 Aug 2022 14:18:37: 2000000 INFO @ Tue, 02 Aug 2022 14:18:39: 8000000 INFO @ Tue, 02 Aug 2022 14:18:43: 3000000 INFO @ Tue, 02 Aug 2022 14:18:45: 9000000 INFO @ Tue, 02 Aug 2022 14:18:50: 4000000 INFO @ Tue, 02 Aug 2022 14:18:51: 10000000 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 14:18:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206506/SRX15206506.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206506/SRX15206506.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206506/SRX15206506.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206506/SRX15206506.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 14:18:53: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:18:53: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:18:55: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:18:55: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:18:55: #1 total tags in treatment: 10683156 INFO @ Tue, 02 Aug 2022 14:18:55: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:18:55: #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 14:18:55: #1 tags after filtering in treatment: 10683156 INFO @ Tue, 02 Aug 2022 14:18:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:18:55: #1 finished! INFO @ Tue, 02 Aug 2022 14:18:55: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:18:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:18:56: 5000000 INFO @ Tue, 02 Aug 2022 14:18:56: #2 number of paired peaks: 843 WARNING @ Tue, 02 Aug 2022 14:18:56: Fewer paired peaks (843) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 843 pairs to build model! INFO @ Tue, 02 Aug 2022 14:18:56: start model_add_line... INFO @ Tue, 02 Aug 2022 14:18:56: start X-correlation... INFO @ Tue, 02 Aug 2022 14:18:56: end of X-cor INFO @ Tue, 02 Aug 2022 14:18:56: #2 finished! INFO @ Tue, 02 Aug 2022 14:18:56: #2 predicted fragment length is 86 bps INFO @ Tue, 02 Aug 2022 14:18:56: #2 alternative fragment length(s) may be 86 bps INFO @ Tue, 02 Aug 2022 14:18:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206506/SRX15206506.05_model.r WARNING @ Tue, 02 Aug 2022 14:18:56: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:18:56: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Tue, 02 Aug 2022 14:18:56: #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 14:18:56: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:18:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:19:00: 1000000 INFO @ Tue, 02 Aug 2022 14:19:02: 6000000 INFO @ Tue, 02 Aug 2022 14:19:06: 2000000 INFO @ Tue, 02 Aug 2022 14:19:08: 7000000 INFO @ Tue, 02 Aug 2022 14:19:12: 3000000 INFO @ Tue, 02 Aug 2022 14:19:14: 8000000 INFO @ Tue, 02 Aug 2022 14:19:17: 4000000 INFO @ Tue, 02 Aug 2022 14:19:18: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:19:20: 9000000 INFO @ Tue, 02 Aug 2022 14:19:23: 5000000 INFO @ Tue, 02 Aug 2022 14:19:26: 10000000 INFO @ Tue, 02 Aug 2022 14:19:29: 6000000 INFO @ Tue, 02 Aug 2022 14:19:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206506/SRX15206506.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:19:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206506/SRX15206506.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:19:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206506/SRX15206506.05_summits.bed INFO @ Tue, 02 Aug 2022 14:19:29: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3707 records, 4 fields): 40 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:19:30: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:19:30: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:19:30: #1 total tags in treatment: 10683156 INFO @ Tue, 02 Aug 2022 14:19:30: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:19:30: #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 14:19:30: #1 tags after filtering in treatment: 10683156 INFO @ Tue, 02 Aug 2022 14:19:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:19:30: #1 finished! INFO @ Tue, 02 Aug 2022 14:19:30: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:19:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:19:31: #2 number of paired peaks: 843 WARNING @ Tue, 02 Aug 2022 14:19:31: Fewer paired peaks (843) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 843 pairs to build model! INFO @ Tue, 02 Aug 2022 14:19:31: start model_add_line... INFO @ Tue, 02 Aug 2022 14:19:31: start X-correlation... INFO @ Tue, 02 Aug 2022 14:19:31: end of X-cor INFO @ Tue, 02 Aug 2022 14:19:31: #2 finished! INFO @ Tue, 02 Aug 2022 14:19:31: #2 predicted fragment length is 86 bps INFO @ Tue, 02 Aug 2022 14:19:31: #2 alternative fragment length(s) may be 86 bps INFO @ Tue, 02 Aug 2022 14:19:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206506/SRX15206506.10_model.r WARNING @ Tue, 02 Aug 2022 14:19:31: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:19:31: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Tue, 02 Aug 2022 14:19:31: #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 14:19:31: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:19:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:19:35: 7000000 INFO @ Tue, 02 Aug 2022 14:19:40: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:19:45: 9000000 INFO @ Tue, 02 Aug 2022 14:19:50: 10000000 INFO @ Tue, 02 Aug 2022 14:19:52: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:19:54: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:19:54: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:19:54: #1 total tags in treatment: 10683156 INFO @ Tue, 02 Aug 2022 14:19:54: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:19:54: #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 14:19:54: #1 tags after filtering in treatment: 10683156 INFO @ Tue, 02 Aug 2022 14:19:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:19:54: #1 finished! INFO @ Tue, 02 Aug 2022 14:19:54: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:19:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:19:55: #2 number of paired peaks: 843 WARNING @ Tue, 02 Aug 2022 14:19:55: Fewer paired peaks (843) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 843 pairs to build model! INFO @ Tue, 02 Aug 2022 14:19:55: start model_add_line... INFO @ Tue, 02 Aug 2022 14:19:55: start X-correlation... INFO @ Tue, 02 Aug 2022 14:19:55: end of X-cor INFO @ Tue, 02 Aug 2022 14:19:55: #2 finished! INFO @ Tue, 02 Aug 2022 14:19:55: #2 predicted fragment length is 86 bps INFO @ Tue, 02 Aug 2022 14:19:55: #2 alternative fragment length(s) may be 86 bps INFO @ Tue, 02 Aug 2022 14:19:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206506/SRX15206506.20_model.r WARNING @ Tue, 02 Aug 2022 14:19:55: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:19:55: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Tue, 02 Aug 2022 14:19:55: #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 14:19:55: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:19:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:20:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206506/SRX15206506.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:20:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206506/SRX15206506.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:20:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206506/SRX15206506.10_summits.bed INFO @ Tue, 02 Aug 2022 14:20:03: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2155 records, 4 fields): 26 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:20:16: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:20:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206506/SRX15206506.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:20:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206506/SRX15206506.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:20:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206506/SRX15206506.20_summits.bed INFO @ Tue, 02 Aug 2022 14:20:27: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1131 records, 4 fields): 80 millis CompletedMACS2peakCalling