Job ID = 6527824 SRX = SRX287773 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:28:07 prefetch.2.10.7: 1) Downloading 'SRR869962'... 2020-06-29T13:28:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:32:20 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:32:20 prefetch.2.10.7: 1) 'SRR869962' was downloaded successfully Read 26924228 spots for SRR869962/SRR869962.sra Written 26924228 spots for SRR869962/SRR869962.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: 00:11:38 26924228 reads; of these: 26924228 (100.00%) were unpaired; of these: 1125811 (4.18%) aligned 0 times 17097115 (63.50%) aligned exactly 1 time 8701302 (32.32%) aligned >1 times 95.82% overall alignment rate Time searching: 00:11:38 Overall time: 00:11:38 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] 3993141 / 25798417 = 0.1548 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 22:58:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287773/SRX287773.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287773/SRX287773.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287773/SRX287773.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287773/SRX287773.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 22:58:07: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:58:07: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:58:12: 1000000 INFO @ Mon, 29 Jun 2020 22:58:18: 2000000 INFO @ Mon, 29 Jun 2020 22:58:24: 3000000 INFO @ Mon, 29 Jun 2020 22:58:30: 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 @ Mon, 29 Jun 2020 22:58:36: 5000000 INFO @ Mon, 29 Jun 2020 22:58:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287773/SRX287773.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287773/SRX287773.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287773/SRX287773.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287773/SRX287773.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 22:58:37: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:58:37: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:58:42: 6000000 INFO @ Mon, 29 Jun 2020 22:58:44: 1000000 INFO @ Mon, 29 Jun 2020 22:58:49: 7000000 INFO @ Mon, 29 Jun 2020 22:58:51: 2000000 INFO @ Mon, 29 Jun 2020 22:58:56: 8000000 INFO @ Mon, 29 Jun 2020 22:58:58: 3000000 INFO @ Mon, 29 Jun 2020 22:59:03: 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 @ Mon, 29 Jun 2020 22:59:05: 4000000 INFO @ Mon, 29 Jun 2020 22:59:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287773/SRX287773.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287773/SRX287773.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287773/SRX287773.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287773/SRX287773.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 22:59:07: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:59:07: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:59:10: 10000000 INFO @ Mon, 29 Jun 2020 22:59:12: 5000000 INFO @ Mon, 29 Jun 2020 22:59:14: 1000000 INFO @ Mon, 29 Jun 2020 22:59:17: 11000000 INFO @ Mon, 29 Jun 2020 22:59:19: 6000000 INFO @ Mon, 29 Jun 2020 22:59:21: 2000000 INFO @ Mon, 29 Jun 2020 22:59:25: 12000000 INFO @ Mon, 29 Jun 2020 22:59:27: 7000000 INFO @ Mon, 29 Jun 2020 22:59:29: 3000000 INFO @ Mon, 29 Jun 2020 22:59:32: 13000000 INFO @ Mon, 29 Jun 2020 22:59:35: 8000000 INFO @ Mon, 29 Jun 2020 22:59:36: 4000000 INFO @ Mon, 29 Jun 2020 22:59:39: 14000000 INFO @ Mon, 29 Jun 2020 22:59:42: 9000000 INFO @ Mon, 29 Jun 2020 22:59:43: 5000000 INFO @ Mon, 29 Jun 2020 22:59:46: 15000000 INFO @ Mon, 29 Jun 2020 22:59:49: 10000000 INFO @ Mon, 29 Jun 2020 22:59:50: 6000000 INFO @ Mon, 29 Jun 2020 22:59:54: 16000000 INFO @ Mon, 29 Jun 2020 22:59:57: 11000000 INFO @ Mon, 29 Jun 2020 22:59:58: 7000000 INFO @ Mon, 29 Jun 2020 23:00:01: 17000000 INFO @ Mon, 29 Jun 2020 23:00:04: 12000000 INFO @ Mon, 29 Jun 2020 23:00:05: 8000000 INFO @ Mon, 29 Jun 2020 23:00:08: 18000000 INFO @ Mon, 29 Jun 2020 23:00:11: 13000000 INFO @ Mon, 29 Jun 2020 23:00:11: 9000000 INFO @ Mon, 29 Jun 2020 23:00:15: 19000000 INFO @ Mon, 29 Jun 2020 23:00:18: 14000000 INFO @ Mon, 29 Jun 2020 23:00:18: 10000000 INFO @ Mon, 29 Jun 2020 23:00:21: 20000000 INFO @ Mon, 29 Jun 2020 23:00:25: 15000000 INFO @ Mon, 29 Jun 2020 23:00:25: 11000000 INFO @ Mon, 29 Jun 2020 23:00:28: 21000000 INFO @ Mon, 29 Jun 2020 23:00:33: 12000000 INFO @ Mon, 29 Jun 2020 23:00:33: 16000000 INFO @ Mon, 29 Jun 2020 23:00:34: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:00:34: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:00:34: #1 total tags in treatment: 21805276 INFO @ Mon, 29 Jun 2020 23:00:34: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:00:34: #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 23:00:34: #1 tags after filtering in treatment: 21805276 INFO @ Mon, 29 Jun 2020 23:00:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:00:34: #1 finished! INFO @ Mon, 29 Jun 2020 23:00:34: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:00:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:00:36: #2 number of paired peaks: 156 WARNING @ Mon, 29 Jun 2020 23:00:36: Fewer paired peaks (156) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 156 pairs to build model! INFO @ Mon, 29 Jun 2020 23:00:36: start model_add_line... INFO @ Mon, 29 Jun 2020 23:00:36: start X-correlation... INFO @ Mon, 29 Jun 2020 23:00:36: end of X-cor INFO @ Mon, 29 Jun 2020 23:00:36: #2 finished! INFO @ Mon, 29 Jun 2020 23:00:36: #2 predicted fragment length is 41 bps INFO @ Mon, 29 Jun 2020 23:00:36: #2 alternative fragment length(s) may be 41 bps INFO @ Mon, 29 Jun 2020 23:00:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287773/SRX287773.05_model.r WARNING @ Mon, 29 Jun 2020 23:00:36: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:00:36: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Mon, 29 Jun 2020 23:00:36: #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 23:00:36: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:00:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:00:39: 13000000 INFO @ Mon, 29 Jun 2020 23:00:40: 17000000 INFO @ Mon, 29 Jun 2020 23:00:46: 14000000 INFO @ Mon, 29 Jun 2020 23:00:47: 18000000 INFO @ Mon, 29 Jun 2020 23:00:53: 15000000 INFO @ Mon, 29 Jun 2020 23:00:54: 19000000 INFO @ Mon, 29 Jun 2020 23:01:00: 16000000 INFO @ Mon, 29 Jun 2020 23:01:01: 20000000 INFO @ Mon, 29 Jun 2020 23:01:07: 17000000 INFO @ Mon, 29 Jun 2020 23:01:08: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:01:14: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:01:14: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:01:14: #1 total tags in treatment: 21805276 INFO @ Mon, 29 Jun 2020 23:01:14: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:01:14: #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 23:01:14: 18000000 INFO @ Mon, 29 Jun 2020 23:01:14: #1 tags after filtering in treatment: 21805276 INFO @ Mon, 29 Jun 2020 23:01:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:01:14: #1 finished! INFO @ Mon, 29 Jun 2020 23:01:14: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:01:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:01:16: #2 number of paired peaks: 156 WARNING @ Mon, 29 Jun 2020 23:01:16: Fewer paired peaks (156) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 156 pairs to build model! INFO @ Mon, 29 Jun 2020 23:01:16: start model_add_line... INFO @ Mon, 29 Jun 2020 23:01:16: start X-correlation... INFO @ Mon, 29 Jun 2020 23:01:16: end of X-cor INFO @ Mon, 29 Jun 2020 23:01:16: #2 finished! INFO @ Mon, 29 Jun 2020 23:01:16: #2 predicted fragment length is 41 bps INFO @ Mon, 29 Jun 2020 23:01:16: #2 alternative fragment length(s) may be 41 bps INFO @ Mon, 29 Jun 2020 23:01:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287773/SRX287773.10_model.r WARNING @ Mon, 29 Jun 2020 23:01:16: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:01:16: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Mon, 29 Jun 2020 23:01:16: #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 23:01:16: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:01:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:01:19: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:01:21: 19000000 INFO @ Mon, 29 Jun 2020 23:01:27: 20000000 INFO @ Mon, 29 Jun 2020 23:01:34: 21000000 INFO @ Mon, 29 Jun 2020 23:01:39: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:01:39: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:01:39: #1 total tags in treatment: 21805276 INFO @ Mon, 29 Jun 2020 23:01:39: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:01:39: #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 23:01:39: #1 tags after filtering in treatment: 21805276 INFO @ Mon, 29 Jun 2020 23:01:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:01:39: #1 finished! INFO @ Mon, 29 Jun 2020 23:01:39: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:01:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:01:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287773/SRX287773.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:01:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287773/SRX287773.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:01:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287773/SRX287773.05_summits.bed INFO @ Mon, 29 Jun 2020 23:01:40: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (2250 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:01:41: #2 number of paired peaks: 156 WARNING @ Mon, 29 Jun 2020 23:01:41: Fewer paired peaks (156) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 156 pairs to build model! INFO @ Mon, 29 Jun 2020 23:01:41: start model_add_line... INFO @ Mon, 29 Jun 2020 23:01:41: start X-correlation... INFO @ Mon, 29 Jun 2020 23:01:41: end of X-cor INFO @ Mon, 29 Jun 2020 23:01:41: #2 finished! INFO @ Mon, 29 Jun 2020 23:01:41: #2 predicted fragment length is 41 bps INFO @ Mon, 29 Jun 2020 23:01:41: #2 alternative fragment length(s) may be 41 bps INFO @ Mon, 29 Jun 2020 23:01:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287773/SRX287773.20_model.r WARNING @ Mon, 29 Jun 2020 23:01:41: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:01:41: #2 You may need to consider one of the other alternative d(s): 41 WARNING @ Mon, 29 Jun 2020 23:01:41: #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 23:01:41: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:01:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:01:57: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:02:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287773/SRX287773.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:02:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287773/SRX287773.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:02:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287773/SRX287773.10_summits.bed INFO @ Mon, 29 Jun 2020 23:02:18: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1884 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:02:22: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:02:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287773/SRX287773.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:02:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287773/SRX287773.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:02:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287773/SRX287773.20_summits.bed INFO @ Mon, 29 Jun 2020 23:02:43: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1458 records, 4 fields): 4 millis CompletedMACS2peakCalling