Job ID = 6457203 SRX = SRX4563525 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:29:10 prefetch.2.10.7: 1) Downloading 'SRR7706252'... 2020-06-21T11:29:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:32:36 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:32:37 prefetch.2.10.7: 'SRR7706252' is valid 2020-06-21T11:32:37 prefetch.2.10.7: 1) 'SRR7706252' was downloaded successfully Read 14010113 spots for SRR7706252/SRR7706252.sra Written 14010113 spots for SRR7706252/SRR7706252.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: 00:03:50 14010113 reads; of these: 14010113 (100.00%) were unpaired; of these: 4305088 (30.73%) aligned 0 times 7007964 (50.02%) aligned exactly 1 time 2697061 (19.25%) aligned >1 times 69.27% overall alignment rate Time searching: 00:03:50 Overall time: 00:03:50 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_rmdupse_core] 1782027 / 9705025 = 0.1836 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 20:40:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4563525/SRX4563525.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4563525/SRX4563525.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4563525/SRX4563525.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4563525/SRX4563525.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 20:40:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:40:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:40:10: 1000000 INFO @ Sun, 21 Jun 2020 20:40:16: 2000000 INFO @ Sun, 21 Jun 2020 20:40:23: 3000000 INFO @ Sun, 21 Jun 2020 20:40:30: 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 @ Sun, 21 Jun 2020 20:40:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4563525/SRX4563525.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4563525/SRX4563525.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4563525/SRX4563525.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4563525/SRX4563525.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 20:40:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:40:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:40:38: 5000000 INFO @ Sun, 21 Jun 2020 20:40:40: 1000000 INFO @ Sun, 21 Jun 2020 20:40:46: 6000000 INFO @ Sun, 21 Jun 2020 20:40:48: 2000000 INFO @ Sun, 21 Jun 2020 20:40:54: 7000000 INFO @ Sun, 21 Jun 2020 20:40:55: 3000000 INFO @ Sun, 21 Jun 2020 20:41:01: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:41:01: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:41:01: #1 total tags in treatment: 7922998 INFO @ Sun, 21 Jun 2020 20:41:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:41:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 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 20:41:02: 4000000 INFO @ Sun, 21 Jun 2020 20:41:02: #1 tags after filtering in treatment: 7922876 INFO @ Sun, 21 Jun 2020 20:41:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:41:02: #1 finished! INFO @ Sun, 21 Jun 2020 20:41:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:41:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:41:02: #2 number of paired peaks: 370 WARNING @ Sun, 21 Jun 2020 20:41:02: Fewer paired peaks (370) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 370 pairs to build model! INFO @ Sun, 21 Jun 2020 20:41:02: start model_add_line... INFO @ Sun, 21 Jun 2020 20:41:02: start X-correlation... INFO @ Sun, 21 Jun 2020 20:41:02: end of X-cor INFO @ Sun, 21 Jun 2020 20:41:02: #2 finished! INFO @ Sun, 21 Jun 2020 20:41:02: #2 predicted fragment length is 63 bps INFO @ Sun, 21 Jun 2020 20:41:02: #2 alternative fragment length(s) may be 63,585 bps INFO @ Sun, 21 Jun 2020 20:41:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4563525/SRX4563525.05_model.r WARNING @ Sun, 21 Jun 2020 20:41:02: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:41:02: #2 You may need to consider one of the other alternative d(s): 63,585 WARNING @ Sun, 21 Jun 2020 20:41:02: #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 20:41:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:41:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:41:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4563525/SRX4563525.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4563525/SRX4563525.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4563525/SRX4563525.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4563525/SRX4563525.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 20:41:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:41:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:41:09: 5000000 INFO @ Sun, 21 Jun 2020 20:41:11: 1000000 INFO @ Sun, 21 Jun 2020 20:41:16: 6000000 INFO @ Sun, 21 Jun 2020 20:41:18: 2000000 INFO @ Sun, 21 Jun 2020 20:41:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:41:24: 7000000 INFO @ Sun, 21 Jun 2020 20:41:26: 3000000 INFO @ Sun, 21 Jun 2020 20:41:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4563525/SRX4563525.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:41:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4563525/SRX4563525.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:41:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4563525/SRX4563525.05_summits.bed INFO @ Sun, 21 Jun 2020 20:41:27: Done! pass1 - making usageList (540 chroms): 1 millis pass2 - checking and writing primary data (2338 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:41:32: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:41:32: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:41:32: #1 total tags in treatment: 7922998 INFO @ Sun, 21 Jun 2020 20:41:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:41:32: #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 20:41:32: #1 tags after filtering in treatment: 7922876 INFO @ Sun, 21 Jun 2020 20:41:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:41:32: #1 finished! INFO @ Sun, 21 Jun 2020 20:41:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:41:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:41:33: #2 number of paired peaks: 370 WARNING @ Sun, 21 Jun 2020 20:41:33: Fewer paired peaks (370) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 370 pairs to build model! INFO @ Sun, 21 Jun 2020 20:41:33: start model_add_line... INFO @ Sun, 21 Jun 2020 20:41:33: start X-correlation... INFO @ Sun, 21 Jun 2020 20:41:33: end of X-cor INFO @ Sun, 21 Jun 2020 20:41:33: #2 finished! INFO @ Sun, 21 Jun 2020 20:41:33: #2 predicted fragment length is 63 bps INFO @ Sun, 21 Jun 2020 20:41:33: #2 alternative fragment length(s) may be 63,585 bps INFO @ Sun, 21 Jun 2020 20:41:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4563525/SRX4563525.10_model.r WARNING @ Sun, 21 Jun 2020 20:41:33: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:41:33: #2 You may need to consider one of the other alternative d(s): 63,585 WARNING @ Sun, 21 Jun 2020 20:41:33: #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 20:41:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:41:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:41:33: 4000000 INFO @ Sun, 21 Jun 2020 20:41:40: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:41:47: 6000000 INFO @ Sun, 21 Jun 2020 20:41:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:41:54: 7000000 INFO @ Sun, 21 Jun 2020 20:41:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4563525/SRX4563525.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:41:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4563525/SRX4563525.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:41:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4563525/SRX4563525.10_summits.bed INFO @ Sun, 21 Jun 2020 20:41:58: Done! pass1 - making usageList (395 chroms): 1 millis pass2 - checking and writing primary data (1071 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:42:01: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:42:01: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:42:01: #1 total tags in treatment: 7922998 INFO @ Sun, 21 Jun 2020 20:42:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:42:01: #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 20:42:01: #1 tags after filtering in treatment: 7922876 INFO @ Sun, 21 Jun 2020 20:42:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:42:01: #1 finished! INFO @ Sun, 21 Jun 2020 20:42:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:42:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:42:02: #2 number of paired peaks: 370 WARNING @ Sun, 21 Jun 2020 20:42:02: Fewer paired peaks (370) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 370 pairs to build model! INFO @ Sun, 21 Jun 2020 20:42:02: start model_add_line... INFO @ Sun, 21 Jun 2020 20:42:02: start X-correlation... INFO @ Sun, 21 Jun 2020 20:42:02: end of X-cor INFO @ Sun, 21 Jun 2020 20:42:02: #2 finished! INFO @ Sun, 21 Jun 2020 20:42:02: #2 predicted fragment length is 63 bps INFO @ Sun, 21 Jun 2020 20:42:02: #2 alternative fragment length(s) may be 63,585 bps INFO @ Sun, 21 Jun 2020 20:42:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4563525/SRX4563525.20_model.r WARNING @ Sun, 21 Jun 2020 20:42:02: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:42:02: #2 You may need to consider one of the other alternative d(s): 63,585 WARNING @ Sun, 21 Jun 2020 20:42:02: #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 20:42:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:42:02: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:42:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:42:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4563525/SRX4563525.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:42:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4563525/SRX4563525.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:42:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4563525/SRX4563525.20_summits.bed INFO @ Sun, 21 Jun 2020 20:42:26: Done! pass1 - making usageList (143 chroms): 1 millis pass2 - checking and writing primary data (255 records, 4 fields): 6 millis CompletedMACS2peakCalling