Job ID = 6498432 SRX = SRX495289 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:23:32 prefetch.2.10.7: 1) Downloading 'SRR1198794'... 2020-06-25T23:23:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:26:17 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:26:17 prefetch.2.10.7: 1) 'SRR1198794' was downloaded successfully Read 27233332 spots for SRR1198794/SRR1198794.sra Written 27233332 spots for SRR1198794/SRR1198794.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:14:19 27233332 reads; of these: 27233332 (100.00%) were unpaired; of these: 1366164 (5.02%) aligned 0 times 10467110 (38.43%) aligned exactly 1 time 15400058 (56.55%) aligned >1 times 94.98% overall alignment rate Time searching: 00:14:19 Overall time: 00:14:19 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] 12765412 / 25867168 = 0.4935 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 @ Fri, 26 Jun 2020 08:48:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495289/SRX495289.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495289/SRX495289.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495289/SRX495289.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495289/SRX495289.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 @ Fri, 26 Jun 2020 08:48:14: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:48:14: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:48:21: 1000000 INFO @ Fri, 26 Jun 2020 08:48:27: 2000000 INFO @ Fri, 26 Jun 2020 08:48:33: 3000000 INFO @ Fri, 26 Jun 2020 08:48:39: 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 @ Fri, 26 Jun 2020 08:48:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495289/SRX495289.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495289/SRX495289.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495289/SRX495289.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495289/SRX495289.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 @ Fri, 26 Jun 2020 08:48:44: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:48:44: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:48:46: 5000000 INFO @ Fri, 26 Jun 2020 08:48:51: 1000000 INFO @ Fri, 26 Jun 2020 08:48:52: 6000000 INFO @ Fri, 26 Jun 2020 08:48:58: 2000000 INFO @ Fri, 26 Jun 2020 08:48:59: 7000000 INFO @ Fri, 26 Jun 2020 08:49:04: 3000000 INFO @ Fri, 26 Jun 2020 08:49:05: 8000000 INFO @ Fri, 26 Jun 2020 08:49:11: 4000000 INFO @ Fri, 26 Jun 2020 08:49:12: 9000000 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 @ Fri, 26 Jun 2020 08:49:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495289/SRX495289.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495289/SRX495289.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495289/SRX495289.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495289/SRX495289.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 @ Fri, 26 Jun 2020 08:49:15: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:49:15: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:49:18: 5000000 INFO @ Fri, 26 Jun 2020 08:49:19: 10000000 INFO @ Fri, 26 Jun 2020 08:49:23: 1000000 INFO @ Fri, 26 Jun 2020 08:49:25: 6000000 INFO @ Fri, 26 Jun 2020 08:49:26: 11000000 INFO @ Fri, 26 Jun 2020 08:49:31: 2000000 INFO @ Fri, 26 Jun 2020 08:49:32: 7000000 INFO @ Fri, 26 Jun 2020 08:49:33: 12000000 INFO @ Fri, 26 Jun 2020 08:49:39: 3000000 INFO @ Fri, 26 Jun 2020 08:49:39: 8000000 INFO @ Fri, 26 Jun 2020 08:49:40: 13000000 INFO @ Fri, 26 Jun 2020 08:49:41: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:49:41: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:49:41: #1 total tags in treatment: 13101756 INFO @ Fri, 26 Jun 2020 08:49:41: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:49:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:49:41: #1 tags after filtering in treatment: 13101756 INFO @ Fri, 26 Jun 2020 08:49:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:49:41: #1 finished! INFO @ Fri, 26 Jun 2020 08:49:41: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:49:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:49:42: #2 number of paired peaks: 2732 INFO @ Fri, 26 Jun 2020 08:49:42: start model_add_line... INFO @ Fri, 26 Jun 2020 08:49:42: start X-correlation... INFO @ Fri, 26 Jun 2020 08:49:42: end of X-cor INFO @ Fri, 26 Jun 2020 08:49:42: #2 finished! INFO @ Fri, 26 Jun 2020 08:49:42: #2 predicted fragment length is 2 bps INFO @ Fri, 26 Jun 2020 08:49:42: #2 alternative fragment length(s) may be 2 bps INFO @ Fri, 26 Jun 2020 08:49:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495289/SRX495289.05_model.r WARNING @ Fri, 26 Jun 2020 08:49:42: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:49:42: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Fri, 26 Jun 2020 08:49:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:49:42: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:49:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:49:46: 9000000 INFO @ Fri, 26 Jun 2020 08:49:46: 4000000 INFO @ Fri, 26 Jun 2020 08:49:53: 10000000 INFO @ Fri, 26 Jun 2020 08:49:54: 5000000 INFO @ Fri, 26 Jun 2020 08:50:00: 11000000 INFO @ Fri, 26 Jun 2020 08:50:02: 6000000 INFO @ Fri, 26 Jun 2020 08:50:07: 12000000 INFO @ Fri, 26 Jun 2020 08:50:09: 7000000 INFO @ Fri, 26 Jun 2020 08:50:11: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:50:14: 13000000 INFO @ Fri, 26 Jun 2020 08:50:15: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:50:15: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:50:15: #1 total tags in treatment: 13101756 INFO @ Fri, 26 Jun 2020 08:50:15: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:50:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:50:15: #1 tags after filtering in treatment: 13101756 INFO @ Fri, 26 Jun 2020 08:50:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:50:15: #1 finished! INFO @ Fri, 26 Jun 2020 08:50:15: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:50:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:50:16: #2 number of paired peaks: 2732 INFO @ Fri, 26 Jun 2020 08:50:16: start model_add_line... INFO @ Fri, 26 Jun 2020 08:50:17: start X-correlation... INFO @ Fri, 26 Jun 2020 08:50:17: end of X-cor INFO @ Fri, 26 Jun 2020 08:50:17: #2 finished! INFO @ Fri, 26 Jun 2020 08:50:17: #2 predicted fragment length is 2 bps INFO @ Fri, 26 Jun 2020 08:50:17: #2 alternative fragment length(s) may be 2 bps INFO @ Fri, 26 Jun 2020 08:50:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495289/SRX495289.10_model.r WARNING @ Fri, 26 Jun 2020 08:50:17: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:50:17: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Fri, 26 Jun 2020 08:50:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:50:17: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:50:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:50:17: 8000000 INFO @ Fri, 26 Jun 2020 08:50:24: 9000000 INFO @ Fri, 26 Jun 2020 08:50:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495289/SRX495289.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:50:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495289/SRX495289.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:50:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495289/SRX495289.05_summits.bed INFO @ Fri, 26 Jun 2020 08:50:25: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:50:31: 10000000 INFO @ Fri, 26 Jun 2020 08:50:38: 11000000 INFO @ Fri, 26 Jun 2020 08:50:45: 12000000 INFO @ Fri, 26 Jun 2020 08:50:45: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:50:52: 13000000 INFO @ Fri, 26 Jun 2020 08:50:53: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:50:53: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:50:53: #1 total tags in treatment: 13101756 INFO @ Fri, 26 Jun 2020 08:50:53: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:50:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:50:53: #1 tags after filtering in treatment: 13101756 INFO @ Fri, 26 Jun 2020 08:50:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:50:53: #1 finished! INFO @ Fri, 26 Jun 2020 08:50:53: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:50:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:50:55: #2 number of paired peaks: 2732 INFO @ Fri, 26 Jun 2020 08:50:55: start model_add_line... INFO @ Fri, 26 Jun 2020 08:50:55: start X-correlation... INFO @ Fri, 26 Jun 2020 08:50:55: end of X-cor INFO @ Fri, 26 Jun 2020 08:50:55: #2 finished! INFO @ Fri, 26 Jun 2020 08:50:55: #2 predicted fragment length is 2 bps INFO @ Fri, 26 Jun 2020 08:50:55: #2 alternative fragment length(s) may be 2 bps INFO @ Fri, 26 Jun 2020 08:50:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495289/SRX495289.20_model.r WARNING @ Fri, 26 Jun 2020 08:50:55: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:50:55: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Fri, 26 Jun 2020 08:50:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:50:55: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:50:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:50:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495289/SRX495289.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:50:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495289/SRX495289.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:50:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495289/SRX495289.10_summits.bed INFO @ Fri, 26 Jun 2020 08:50:59: Done! BigWig に変換しました。 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:51:23: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:51:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495289/SRX495289.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:51:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495289/SRX495289.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:51:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495289/SRX495289.20_summits.bed INFO @ Fri, 26 Jun 2020 08:51:37: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling