Job ID = 6527949 SRX = SRX335515 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T14:19:20 prefetch.2.10.7: 1) Downloading 'SRR952857'... 2020-06-29T14:19:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:21:13 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:21:13 prefetch.2.10.7: 1) 'SRR952857' was downloaded successfully Read 18892168 spots for SRR952857/SRR952857.sra Written 18892168 spots for SRR952857/SRR952857.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: 00:05:42 18892168 reads; of these: 18892168 (100.00%) were unpaired; of these: 2120266 (11.22%) aligned 0 times 12078628 (63.93%) aligned exactly 1 time 4693274 (24.84%) aligned >1 times 88.78% overall alignment rate Time searching: 00:05:42 Overall time: 00:05:42 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] 3854629 / 16771902 = 0.2298 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 @ Mon, 29 Jun 2020 23:38:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX335515/SRX335515.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX335515/SRX335515.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX335515/SRX335515.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX335515/SRX335515.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 @ Mon, 29 Jun 2020 23:38:47: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:38:47: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:38:56: 1000000 INFO @ Mon, 29 Jun 2020 23:39:04: 2000000 INFO @ Mon, 29 Jun 2020 23:39:13: 3000000 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 @ Mon, 29 Jun 2020 23:39:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX335515/SRX335515.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX335515/SRX335515.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX335515/SRX335515.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX335515/SRX335515.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 @ Mon, 29 Jun 2020 23:39:17: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:39:17: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:39:21: 4000000 INFO @ Mon, 29 Jun 2020 23:39:24: 1000000 INFO @ Mon, 29 Jun 2020 23:39:30: 5000000 INFO @ Mon, 29 Jun 2020 23:39:31: 2000000 INFO @ Mon, 29 Jun 2020 23:39:39: 3000000 INFO @ Mon, 29 Jun 2020 23:39:39: 6000000 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 @ Mon, 29 Jun 2020 23:39:46: 4000000 INFO @ Mon, 29 Jun 2020 23:39:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX335515/SRX335515.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX335515/SRX335515.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX335515/SRX335515.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX335515/SRX335515.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 @ Mon, 29 Jun 2020 23:39:47: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:39:47: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:39:47: 7000000 INFO @ Mon, 29 Jun 2020 23:39:54: 5000000 INFO @ Mon, 29 Jun 2020 23:39:55: 1000000 INFO @ Mon, 29 Jun 2020 23:39:56: 8000000 INFO @ Mon, 29 Jun 2020 23:40:02: 6000000 INFO @ Mon, 29 Jun 2020 23:40:04: 2000000 INFO @ Mon, 29 Jun 2020 23:40:05: 9000000 INFO @ Mon, 29 Jun 2020 23:40:11: 7000000 INFO @ Mon, 29 Jun 2020 23:40:12: 3000000 INFO @ Mon, 29 Jun 2020 23:40:14: 10000000 INFO @ Mon, 29 Jun 2020 23:40:19: 8000000 INFO @ Mon, 29 Jun 2020 23:40:21: 4000000 INFO @ Mon, 29 Jun 2020 23:40:23: 11000000 INFO @ Mon, 29 Jun 2020 23:40:27: 9000000 INFO @ Mon, 29 Jun 2020 23:40:29: 5000000 INFO @ Mon, 29 Jun 2020 23:40:31: 12000000 INFO @ Mon, 29 Jun 2020 23:40:35: 10000000 INFO @ Mon, 29 Jun 2020 23:40:37: 6000000 INFO @ Mon, 29 Jun 2020 23:40:39: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:40:39: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:40:39: #1 total tags in treatment: 12917273 INFO @ Mon, 29 Jun 2020 23:40:39: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:40:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:40:39: #1 tags after filtering in treatment: 12917273 INFO @ Mon, 29 Jun 2020 23:40:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:40:39: #1 finished! INFO @ Mon, 29 Jun 2020 23:40:39: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:40:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:40:40: #2 number of paired peaks: 404 WARNING @ Mon, 29 Jun 2020 23:40:40: Fewer paired peaks (404) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 404 pairs to build model! INFO @ Mon, 29 Jun 2020 23:40:40: start model_add_line... INFO @ Mon, 29 Jun 2020 23:40:40: start X-correlation... INFO @ Mon, 29 Jun 2020 23:40:40: end of X-cor INFO @ Mon, 29 Jun 2020 23:40:40: #2 finished! INFO @ Mon, 29 Jun 2020 23:40:40: #2 predicted fragment length is 44 bps INFO @ Mon, 29 Jun 2020 23:40:40: #2 alternative fragment length(s) may be 2,15,44,66,469,475 bps INFO @ Mon, 29 Jun 2020 23:40:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX335515/SRX335515.05_model.r WARNING @ Mon, 29 Jun 2020 23:40:40: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:40:40: #2 You may need to consider one of the other alternative d(s): 2,15,44,66,469,475 WARNING @ Mon, 29 Jun 2020 23:40:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:40:40: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:40:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:40:43: 11000000 INFO @ Mon, 29 Jun 2020 23:40:45: 7000000 INFO @ Mon, 29 Jun 2020 23:40:51: 12000000 INFO @ Mon, 29 Jun 2020 23:40:53: 8000000 INFO @ Mon, 29 Jun 2020 23:40:58: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:40:58: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:40:58: #1 total tags in treatment: 12917273 INFO @ Mon, 29 Jun 2020 23:40:58: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:40:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:40:58: #1 tags after filtering in treatment: 12917273 INFO @ Mon, 29 Jun 2020 23:40:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:40:58: #1 finished! INFO @ Mon, 29 Jun 2020 23:40:58: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:40:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:40:59: #2 number of paired peaks: 404 WARNING @ Mon, 29 Jun 2020 23:40:59: Fewer paired peaks (404) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 404 pairs to build model! INFO @ Mon, 29 Jun 2020 23:40:59: start model_add_line... INFO @ Mon, 29 Jun 2020 23:40:59: start X-correlation... INFO @ Mon, 29 Jun 2020 23:40:59: end of X-cor INFO @ Mon, 29 Jun 2020 23:40:59: #2 finished! INFO @ Mon, 29 Jun 2020 23:40:59: #2 predicted fragment length is 44 bps INFO @ Mon, 29 Jun 2020 23:40:59: #2 alternative fragment length(s) may be 2,15,44,66,469,475 bps INFO @ Mon, 29 Jun 2020 23:40:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX335515/SRX335515.10_model.r WARNING @ Mon, 29 Jun 2020 23:40:59: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:40:59: #2 You may need to consider one of the other alternative d(s): 2,15,44,66,469,475 WARNING @ Mon, 29 Jun 2020 23:40:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:40:59: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:40:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:41:01: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:41:05: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:41:08: 10000000 INFO @ Mon, 29 Jun 2020 23:41:16: 11000000 INFO @ Mon, 29 Jun 2020 23:41:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX335515/SRX335515.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:41:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX335515/SRX335515.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:41:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX335515/SRX335515.05_summits.bed INFO @ Mon, 29 Jun 2020 23:41:18: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2510 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:41:23: 12000000 INFO @ Mon, 29 Jun 2020 23:41:23: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:41:29: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:41:29: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:41:29: #1 total tags in treatment: 12917273 INFO @ Mon, 29 Jun 2020 23:41:29: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:41:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:41:30: #1 tags after filtering in treatment: 12917273 INFO @ Mon, 29 Jun 2020 23:41:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:41:30: #1 finished! INFO @ Mon, 29 Jun 2020 23:41:30: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:41:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:41:30: #2 number of paired peaks: 404 WARNING @ Mon, 29 Jun 2020 23:41:30: Fewer paired peaks (404) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 404 pairs to build model! INFO @ Mon, 29 Jun 2020 23:41:30: start model_add_line... INFO @ Mon, 29 Jun 2020 23:41:31: start X-correlation... INFO @ Mon, 29 Jun 2020 23:41:31: end of X-cor INFO @ Mon, 29 Jun 2020 23:41:31: #2 finished! INFO @ Mon, 29 Jun 2020 23:41:31: #2 predicted fragment length is 44 bps INFO @ Mon, 29 Jun 2020 23:41:31: #2 alternative fragment length(s) may be 2,15,44,66,469,475 bps INFO @ Mon, 29 Jun 2020 23:41:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX335515/SRX335515.20_model.r WARNING @ Mon, 29 Jun 2020 23:41:31: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:41:31: #2 You may need to consider one of the other alternative d(s): 2,15,44,66,469,475 WARNING @ Mon, 29 Jun 2020 23:41:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:41:31: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:41:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:41:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX335515/SRX335515.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:41:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX335515/SRX335515.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:41:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX335515/SRX335515.10_summits.bed INFO @ Mon, 29 Jun 2020 23:41:36: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1182 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:41:54: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:42:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX335515/SRX335515.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:42:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX335515/SRX335515.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:42:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX335515/SRX335515.20_summits.bed INFO @ Mon, 29 Jun 2020 23:42:07: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (212 records, 4 fields): 1 millis CompletedMACS2peakCalling