Job ID = 6626645 SRX = SRX7351006 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 27272833 spots for SRR10673636/SRR10673636.sra Written 27272833 spots for SRR10673636/SRR10673636.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626811 ("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: 00:09:31 27272833 reads; of these: 27272833 (100.00%) were unpaired; of these: 770046 (2.82%) aligned 0 times 21236731 (77.87%) aligned exactly 1 time 5266056 (19.31%) aligned >1 times 97.18% overall alignment rate Time searching: 00:09:31 Overall time: 00:09:31 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 12 files... [bam_rmdupse_core] 6272969 / 26502787 = 0.2367 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 08:24:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7351006/SRX7351006.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7351006/SRX7351006.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7351006/SRX7351006.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7351006/SRX7351006.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, 14 Jul 2020 08:24:20: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:24:20: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:24:26: 1000000 INFO @ Tue, 14 Jul 2020 08:24:33: 2000000 INFO @ Tue, 14 Jul 2020 08:24:40: 3000000 INFO @ Tue, 14 Jul 2020 08:24:47: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 08:24:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7351006/SRX7351006.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7351006/SRX7351006.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7351006/SRX7351006.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7351006/SRX7351006.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, 14 Jul 2020 08:24:50: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:24:50: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:24:54: 5000000 INFO @ Tue, 14 Jul 2020 08:24:56: 1000000 INFO @ Tue, 14 Jul 2020 08:25:01: 6000000 INFO @ Tue, 14 Jul 2020 08:25:03: 2000000 INFO @ Tue, 14 Jul 2020 08:25:09: 7000000 INFO @ Tue, 14 Jul 2020 08:25:10: 3000000 INFO @ Tue, 14 Jul 2020 08:25:16: 8000000 INFO @ Tue, 14 Jul 2020 08:25:17: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 08:25:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7351006/SRX7351006.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7351006/SRX7351006.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7351006/SRX7351006.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7351006/SRX7351006.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, 14 Jul 2020 08:25:19: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:25:19: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:25:23: 9000000 INFO @ Tue, 14 Jul 2020 08:25:23: 5000000 INFO @ Tue, 14 Jul 2020 08:25:26: 1000000 INFO @ Tue, 14 Jul 2020 08:25:30: 6000000 INFO @ Tue, 14 Jul 2020 08:25:31: 10000000 INFO @ Tue, 14 Jul 2020 08:25:33: 2000000 INFO @ Tue, 14 Jul 2020 08:25:37: 7000000 INFO @ Tue, 14 Jul 2020 08:25:38: 11000000 INFO @ Tue, 14 Jul 2020 08:25:40: 3000000 INFO @ Tue, 14 Jul 2020 08:25:44: 8000000 INFO @ Tue, 14 Jul 2020 08:25:45: 12000000 INFO @ Tue, 14 Jul 2020 08:25:47: 4000000 INFO @ Tue, 14 Jul 2020 08:25:51: 9000000 INFO @ Tue, 14 Jul 2020 08:25:52: 13000000 INFO @ Tue, 14 Jul 2020 08:25:53: 5000000 INFO @ Tue, 14 Jul 2020 08:25:58: 10000000 INFO @ Tue, 14 Jul 2020 08:26:00: 14000000 INFO @ Tue, 14 Jul 2020 08:26:00: 6000000 INFO @ Tue, 14 Jul 2020 08:26:04: 11000000 INFO @ Tue, 14 Jul 2020 08:26:07: 15000000 INFO @ Tue, 14 Jul 2020 08:26:07: 7000000 INFO @ Tue, 14 Jul 2020 08:26:11: 12000000 INFO @ Tue, 14 Jul 2020 08:26:14: 8000000 INFO @ Tue, 14 Jul 2020 08:26:14: 16000000 INFO @ Tue, 14 Jul 2020 08:26:18: 13000000 INFO @ Tue, 14 Jul 2020 08:26:20: 9000000 INFO @ Tue, 14 Jul 2020 08:26:21: 17000000 INFO @ Tue, 14 Jul 2020 08:26:25: 14000000 INFO @ Tue, 14 Jul 2020 08:26:27: 10000000 INFO @ Tue, 14 Jul 2020 08:26:29: 18000000 INFO @ Tue, 14 Jul 2020 08:26:31: 15000000 INFO @ Tue, 14 Jul 2020 08:26:34: 11000000 INFO @ Tue, 14 Jul 2020 08:26:36: 19000000 INFO @ Tue, 14 Jul 2020 08:26:38: 16000000 INFO @ Tue, 14 Jul 2020 08:26:40: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 08:26:43: 20000000 INFO @ Tue, 14 Jul 2020 08:26:45: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:26:45: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:26:45: #1 total tags in treatment: 20229818 INFO @ Tue, 14 Jul 2020 08:26:45: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:26:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:26:45: 17000000 INFO @ Tue, 14 Jul 2020 08:26:45: #1 tags after filtering in treatment: 20229818 INFO @ Tue, 14 Jul 2020 08:26:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:26:45: #1 finished! INFO @ Tue, 14 Jul 2020 08:26:45: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:26:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:26:47: 13000000 INFO @ Tue, 14 Jul 2020 08:26:47: #2 number of paired peaks: 4834 INFO @ Tue, 14 Jul 2020 08:26:47: start model_add_line... INFO @ Tue, 14 Jul 2020 08:26:47: start X-correlation... INFO @ Tue, 14 Jul 2020 08:26:47: end of X-cor INFO @ Tue, 14 Jul 2020 08:26:47: #2 finished! INFO @ Tue, 14 Jul 2020 08:26:47: #2 predicted fragment length is 132 bps INFO @ Tue, 14 Jul 2020 08:26:47: #2 alternative fragment length(s) may be 4,132 bps INFO @ Tue, 14 Jul 2020 08:26:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7351006/SRX7351006.05_model.r WARNING @ Tue, 14 Jul 2020 08:26:47: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:26:47: #2 You may need to consider one of the other alternative d(s): 4,132 WARNING @ Tue, 14 Jul 2020 08:26:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:26:47: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:26:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:26:51: 18000000 INFO @ Tue, 14 Jul 2020 08:26:53: 14000000 INFO @ Tue, 14 Jul 2020 08:26:58: 19000000 INFO @ Tue, 14 Jul 2020 08:26:59: 15000000 INFO @ Tue, 14 Jul 2020 08:27:04: 20000000 INFO @ Tue, 14 Jul 2020 08:27:06: 16000000 INFO @ Tue, 14 Jul 2020 08:27:06: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:27:06: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:27:06: #1 total tags in treatment: 20229818 INFO @ Tue, 14 Jul 2020 08:27:06: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:27:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:27:06: #1 tags after filtering in treatment: 20229818 INFO @ Tue, 14 Jul 2020 08:27:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:27:06: #1 finished! INFO @ Tue, 14 Jul 2020 08:27:06: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:27:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:27:08: #2 number of paired peaks: 4834 INFO @ Tue, 14 Jul 2020 08:27:08: start model_add_line... INFO @ Tue, 14 Jul 2020 08:27:08: start X-correlation... INFO @ Tue, 14 Jul 2020 08:27:08: end of X-cor INFO @ Tue, 14 Jul 2020 08:27:08: #2 finished! INFO @ Tue, 14 Jul 2020 08:27:08: #2 predicted fragment length is 132 bps INFO @ Tue, 14 Jul 2020 08:27:08: #2 alternative fragment length(s) may be 4,132 bps INFO @ Tue, 14 Jul 2020 08:27:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7351006/SRX7351006.10_model.r WARNING @ Tue, 14 Jul 2020 08:27:08: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:27:08: #2 You may need to consider one of the other alternative d(s): 4,132 WARNING @ Tue, 14 Jul 2020 08:27:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:27:08: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:27:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:27:12: 17000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 08:27:18: 18000000 INFO @ Tue, 14 Jul 2020 08:27:23: 19000000 INFO @ Tue, 14 Jul 2020 08:27:29: 20000000 INFO @ Tue, 14 Jul 2020 08:27:31: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:27:31: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:27:31: #1 total tags in treatment: 20229818 INFO @ Tue, 14 Jul 2020 08:27:31: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:27:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:27:31: #1 tags after filtering in treatment: 20229818 INFO @ Tue, 14 Jul 2020 08:27:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:27:31: #1 finished! INFO @ Tue, 14 Jul 2020 08:27:31: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:27:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:27:33: #2 number of paired peaks: 4834 INFO @ Tue, 14 Jul 2020 08:27:33: start model_add_line... INFO @ Tue, 14 Jul 2020 08:27:33: start X-correlation... INFO @ Tue, 14 Jul 2020 08:27:33: end of X-cor INFO @ Tue, 14 Jul 2020 08:27:33: #2 finished! INFO @ Tue, 14 Jul 2020 08:27:33: #2 predicted fragment length is 132 bps INFO @ Tue, 14 Jul 2020 08:27:33: #2 alternative fragment length(s) may be 4,132 bps INFO @ Tue, 14 Jul 2020 08:27:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7351006/SRX7351006.20_model.r WARNING @ Tue, 14 Jul 2020 08:27:33: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:27:33: #2 You may need to consider one of the other alternative d(s): 4,132 WARNING @ Tue, 14 Jul 2020 08:27:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:27:33: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:27:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:27:33: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:27:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7351006/SRX7351006.05_peaks.xls INFO @ Tue, 14 Jul 2020 08:27:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7351006/SRX7351006.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:27:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7351006/SRX7351006.05_summits.bed INFO @ Tue, 14 Jul 2020 08:27:53: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (14338 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:27:56: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:28:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7351006/SRX7351006.10_peaks.xls INFO @ Tue, 14 Jul 2020 08:28:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7351006/SRX7351006.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:28:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7351006/SRX7351006.10_summits.bed INFO @ Tue, 14 Jul 2020 08:28:18: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (10972 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:28:19: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:28:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7351006/SRX7351006.20_peaks.xls INFO @ Tue, 14 Jul 2020 08:28:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7351006/SRX7351006.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:28:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7351006/SRX7351006.20_summits.bed INFO @ Tue, 14 Jul 2020 08:28:40: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6715 records, 4 fields): 8 millis CompletedMACS2peakCalling