Job ID = 6457892 SRX = SRX4828019 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:02:35 prefetch.2.10.7: 1) Downloading 'SRR7997155'... 2020-06-21T12:02:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:04:35 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:04:35 prefetch.2.10.7: 'SRR7997155' is valid 2020-06-21T12:04:35 prefetch.2.10.7: 1) 'SRR7997155' was downloaded successfully 2020-06-21T12:04:35 prefetch.2.10.7: 'SRR7997155' has 0 unresolved dependencies Read 14515822 spots for SRR7997155/SRR7997155.sra Written 14515822 spots for SRR7997155/SRR7997155.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: 00:03:38 14515822 reads; of these: 14515822 (100.00%) were unpaired; of these: 1195655 (8.24%) aligned 0 times 10333149 (71.19%) aligned exactly 1 time 2987018 (20.58%) aligned >1 times 91.76% overall alignment rate Time searching: 00:03:38 Overall time: 00:03:38 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 3167951 / 13320167 = 0.2378 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 @ Sun, 21 Jun 2020 21:12:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4828019/SRX4828019.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4828019/SRX4828019.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4828019/SRX4828019.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4828019/SRX4828019.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 @ Sun, 21 Jun 2020 21:12:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:12:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:12:09: 1000000 INFO @ Sun, 21 Jun 2020 21:12:15: 2000000 INFO @ Sun, 21 Jun 2020 21:12:20: 3000000 INFO @ Sun, 21 Jun 2020 21:12:26: 4000000 INFO @ Sun, 21 Jun 2020 21:12:31: 5000000 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 @ Sun, 21 Jun 2020 21:12:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4828019/SRX4828019.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4828019/SRX4828019.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4828019/SRX4828019.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4828019/SRX4828019.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 @ Sun, 21 Jun 2020 21:12:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:12:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:12:36: 6000000 INFO @ Sun, 21 Jun 2020 21:12:40: 1000000 INFO @ Sun, 21 Jun 2020 21:12:42: 7000000 INFO @ Sun, 21 Jun 2020 21:12:46: 2000000 INFO @ Sun, 21 Jun 2020 21:12:48: 8000000 INFO @ Sun, 21 Jun 2020 21:12:51: 3000000 INFO @ Sun, 21 Jun 2020 21:12:54: 9000000 INFO @ Sun, 21 Jun 2020 21:12:57: 4000000 INFO @ Sun, 21 Jun 2020 21:12:59: 10000000 INFO @ Sun, 21 Jun 2020 21:13:00: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 21:13:00: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 21:13:00: #1 total tags in treatment: 10152216 INFO @ Sun, 21 Jun 2020 21:13:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:13:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 21:13:01: #1 tags after filtering in treatment: 10152086 INFO @ Sun, 21 Jun 2020 21:13:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:13:01: #1 finished! INFO @ Sun, 21 Jun 2020 21:13:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:13:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:13:02: #2 number of paired peaks: 319 WARNING @ Sun, 21 Jun 2020 21:13:02: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Sun, 21 Jun 2020 21:13:02: start model_add_line... INFO @ Sun, 21 Jun 2020 21:13:02: start X-correlation... INFO @ Sun, 21 Jun 2020 21:13:02: end of X-cor INFO @ Sun, 21 Jun 2020 21:13:02: #2 finished! INFO @ Sun, 21 Jun 2020 21:13:02: #2 predicted fragment length is 64 bps INFO @ Sun, 21 Jun 2020 21:13:02: #2 alternative fragment length(s) may be 4,64 bps INFO @ Sun, 21 Jun 2020 21:13:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4828019/SRX4828019.05_model.r WARNING @ Sun, 21 Jun 2020 21:13:02: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:13:02: #2 You may need to consider one of the other alternative d(s): 4,64 WARNING @ Sun, 21 Jun 2020 21:13:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 21:13:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:13:02: #3 Pre-compute pvalue-qvalue table... 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 @ Sun, 21 Jun 2020 21:13:02: 5000000 INFO @ Sun, 21 Jun 2020 21:13:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4828019/SRX4828019.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4828019/SRX4828019.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4828019/SRX4828019.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4828019/SRX4828019.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 @ Sun, 21 Jun 2020 21:13:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:13:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:13:08: 6000000 INFO @ Sun, 21 Jun 2020 21:13:10: 1000000 INFO @ Sun, 21 Jun 2020 21:13:14: 7000000 INFO @ Sun, 21 Jun 2020 21:13:16: 2000000 INFO @ Sun, 21 Jun 2020 21:13:20: 8000000 INFO @ Sun, 21 Jun 2020 21:13:21: 3000000 INFO @ Sun, 21 Jun 2020 21:13:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:13:25: 9000000 INFO @ Sun, 21 Jun 2020 21:13:27: 4000000 INFO @ Sun, 21 Jun 2020 21:13:31: 10000000 INFO @ Sun, 21 Jun 2020 21:13:32: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 21:13:32: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 21:13:32: #1 total tags in treatment: 10152216 INFO @ Sun, 21 Jun 2020 21:13:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:13:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 21:13:32: #1 tags after filtering in treatment: 10152086 INFO @ Sun, 21 Jun 2020 21:13:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:13:32: #1 finished! INFO @ Sun, 21 Jun 2020 21:13:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:13:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:13:33: 5000000 INFO @ Sun, 21 Jun 2020 21:13:33: #2 number of paired peaks: 319 WARNING @ Sun, 21 Jun 2020 21:13:33: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Sun, 21 Jun 2020 21:13:33: start model_add_line... INFO @ Sun, 21 Jun 2020 21:13:33: start X-correlation... INFO @ Sun, 21 Jun 2020 21:13:33: end of X-cor INFO @ Sun, 21 Jun 2020 21:13:33: #2 finished! INFO @ Sun, 21 Jun 2020 21:13:33: #2 predicted fragment length is 64 bps INFO @ Sun, 21 Jun 2020 21:13:33: #2 alternative fragment length(s) may be 4,64 bps INFO @ Sun, 21 Jun 2020 21:13:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4828019/SRX4828019.10_model.r WARNING @ Sun, 21 Jun 2020 21:13:33: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:13:33: #2 You may need to consider one of the other alternative d(s): 4,64 WARNING @ Sun, 21 Jun 2020 21:13:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 21:13:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:13:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:13:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4828019/SRX4828019.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:13:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4828019/SRX4828019.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:13:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4828019/SRX4828019.05_summits.bed INFO @ Sun, 21 Jun 2020 21:13:36: Done! pass1 - making usageList (402 chroms): 1 millis pass2 - checking and writing primary data (1124 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:13:38: 6000000 INFO @ Sun, 21 Jun 2020 21:13:44: 7000000 INFO @ Sun, 21 Jun 2020 21:13:50: 8000000 INFO @ Sun, 21 Jun 2020 21:13:55: 9000000 INFO @ Sun, 21 Jun 2020 21:13:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:14:00: 10000000 INFO @ Sun, 21 Jun 2020 21:14:01: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 21:14:01: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 21:14:01: #1 total tags in treatment: 10152216 INFO @ Sun, 21 Jun 2020 21:14:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:14:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 21:14:02: #1 tags after filtering in treatment: 10152086 INFO @ Sun, 21 Jun 2020 21:14:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:14:02: #1 finished! INFO @ Sun, 21 Jun 2020 21:14:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:14:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:14:03: #2 number of paired peaks: 319 WARNING @ Sun, 21 Jun 2020 21:14:03: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Sun, 21 Jun 2020 21:14:03: start model_add_line... INFO @ Sun, 21 Jun 2020 21:14:03: start X-correlation... INFO @ Sun, 21 Jun 2020 21:14:03: end of X-cor INFO @ Sun, 21 Jun 2020 21:14:03: #2 finished! INFO @ Sun, 21 Jun 2020 21:14:03: #2 predicted fragment length is 64 bps INFO @ Sun, 21 Jun 2020 21:14:03: #2 alternative fragment length(s) may be 4,64 bps INFO @ Sun, 21 Jun 2020 21:14:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4828019/SRX4828019.20_model.r WARNING @ Sun, 21 Jun 2020 21:14:03: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:14:03: #2 You may need to consider one of the other alternative d(s): 4,64 WARNING @ Sun, 21 Jun 2020 21:14:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 21:14:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:14:03: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:14:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4828019/SRX4828019.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:14:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4828019/SRX4828019.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:14:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4828019/SRX4828019.10_summits.bed INFO @ Sun, 21 Jun 2020 21:14:08: Done! pass1 - making usageList (212 chroms): 1 millis pass2 - checking and writing primary data (481 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:14:26: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:14:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4828019/SRX4828019.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:14:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4828019/SRX4828019.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:14:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4828019/SRX4828019.20_summits.bed INFO @ Sun, 21 Jun 2020 21:14:37: Done! pass1 - making usageList (97 chroms): 1 millis pass2 - checking and writing primary data (213 records, 4 fields): 5 millis CompletedMACS2peakCalling