Job ID = 6454892 SRX = SRX2592480 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:28:59 prefetch.2.10.7: 1) Downloading 'SRR5289757'... 2020-06-21T09:28:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:32:13 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:32:13 prefetch.2.10.7: 'SRR5289757' is valid 2020-06-21T09:32:13 prefetch.2.10.7: 1) 'SRR5289757' was downloaded successfully Read 12337626 spots for SRR5289757/SRR5289757.sra Written 12337626 spots for SRR5289757/SRR5289757.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: 00:02:31 12337626 reads; of these: 12337626 (100.00%) were unpaired; of these: 3819259 (30.96%) aligned 0 times 6265051 (50.78%) aligned exactly 1 time 2253316 (18.26%) aligned >1 times 69.04% overall alignment rate Time searching: 00:02:31 Overall time: 00:02:31 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] 949581 / 8518367 = 0.1115 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 18:37:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592480/SRX2592480.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592480/SRX2592480.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592480/SRX2592480.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592480/SRX2592480.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 18:37:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:37:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:38:05: 1000000 INFO @ Sun, 21 Jun 2020 18:38:12: 2000000 INFO @ Sun, 21 Jun 2020 18:38:18: 3000000 INFO @ Sun, 21 Jun 2020 18:38:24: 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 18:38:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592480/SRX2592480.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592480/SRX2592480.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592480/SRX2592480.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592480/SRX2592480.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 18:38:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:38:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:38:31: 5000000 INFO @ Sun, 21 Jun 2020 18:38:36: 1000000 INFO @ Sun, 21 Jun 2020 18:38:37: 6000000 INFO @ Sun, 21 Jun 2020 18:38:43: 2000000 INFO @ Sun, 21 Jun 2020 18:38:44: 7000000 INFO @ Sun, 21 Jun 2020 18:38:48: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:38:48: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:38:48: #1 total tags in treatment: 7568786 INFO @ Sun, 21 Jun 2020 18:38:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:38:48: #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 18:38:48: #1 tags after filtering in treatment: 7568652 INFO @ Sun, 21 Jun 2020 18:38:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:38:48: #1 finished! INFO @ Sun, 21 Jun 2020 18:38:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:38:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:38:49: #2 number of paired peaks: 574 WARNING @ Sun, 21 Jun 2020 18:38:49: Fewer paired peaks (574) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 574 pairs to build model! INFO @ Sun, 21 Jun 2020 18:38:49: start model_add_line... INFO @ Sun, 21 Jun 2020 18:38:49: start X-correlation... INFO @ Sun, 21 Jun 2020 18:38:49: end of X-cor INFO @ Sun, 21 Jun 2020 18:38:49: #2 finished! INFO @ Sun, 21 Jun 2020 18:38:49: #2 predicted fragment length is 62 bps INFO @ Sun, 21 Jun 2020 18:38:49: #2 alternative fragment length(s) may be 62,581 bps INFO @ Sun, 21 Jun 2020 18:38:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592480/SRX2592480.05_model.r WARNING @ Sun, 21 Jun 2020 18:38:49: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:38:49: #2 You may need to consider one of the other alternative d(s): 62,581 WARNING @ Sun, 21 Jun 2020 18:38:49: #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 18:38:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:38:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:38:50: 3000000 INFO @ Sun, 21 Jun 2020 18:38:56: 4000000 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 18:38:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592480/SRX2592480.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592480/SRX2592480.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592480/SRX2592480.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592480/SRX2592480.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 18:38:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:38:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:39:03: 5000000 INFO @ Sun, 21 Jun 2020 18:39:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:39:06: 1000000 INFO @ Sun, 21 Jun 2020 18:39:10: 6000000 INFO @ Sun, 21 Jun 2020 18:39:12: 2000000 INFO @ Sun, 21 Jun 2020 18:39:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592480/SRX2592480.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:39:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592480/SRX2592480.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:39:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592480/SRX2592480.05_summits.bed INFO @ Sun, 21 Jun 2020 18:39:12: Done! pass1 - making usageList (496 chroms): 1 millis pass2 - checking and writing primary data (1582 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:39:16: 7000000 INFO @ Sun, 21 Jun 2020 18:39:19: 3000000 INFO @ Sun, 21 Jun 2020 18:39:20: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:39:20: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:39:20: #1 total tags in treatment: 7568786 INFO @ Sun, 21 Jun 2020 18:39:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:39:20: #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 18:39:21: #1 tags after filtering in treatment: 7568652 INFO @ Sun, 21 Jun 2020 18:39:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:39:21: #1 finished! INFO @ Sun, 21 Jun 2020 18:39:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:39:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:39:21: #2 number of paired peaks: 574 WARNING @ Sun, 21 Jun 2020 18:39:21: Fewer paired peaks (574) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 574 pairs to build model! INFO @ Sun, 21 Jun 2020 18:39:21: start model_add_line... INFO @ Sun, 21 Jun 2020 18:39:21: start X-correlation... INFO @ Sun, 21 Jun 2020 18:39:21: end of X-cor INFO @ Sun, 21 Jun 2020 18:39:21: #2 finished! INFO @ Sun, 21 Jun 2020 18:39:21: #2 predicted fragment length is 62 bps INFO @ Sun, 21 Jun 2020 18:39:21: #2 alternative fragment length(s) may be 62,581 bps INFO @ Sun, 21 Jun 2020 18:39:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592480/SRX2592480.10_model.r WARNING @ Sun, 21 Jun 2020 18:39:21: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:39:21: #2 You may need to consider one of the other alternative d(s): 62,581 WARNING @ Sun, 21 Jun 2020 18:39:21: #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 18:39:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:39:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:39:25: 4000000 INFO @ Sun, 21 Jun 2020 18:39:32: 5000000 INFO @ Sun, 21 Jun 2020 18:39:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:39:38: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:39:45: 7000000 INFO @ Sun, 21 Jun 2020 18:39:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592480/SRX2592480.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:39:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592480/SRX2592480.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:39:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592480/SRX2592480.10_summits.bed INFO @ Sun, 21 Jun 2020 18:39:45: Done! pass1 - making usageList (242 chroms): 1 millis pass2 - checking and writing primary data (557 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:39:48: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:39:48: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:39:48: #1 total tags in treatment: 7568786 INFO @ Sun, 21 Jun 2020 18:39:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:39:48: #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 18:39:49: #1 tags after filtering in treatment: 7568652 INFO @ Sun, 21 Jun 2020 18:39:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:39:49: #1 finished! INFO @ Sun, 21 Jun 2020 18:39:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:39:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:39:49: #2 number of paired peaks: 574 WARNING @ Sun, 21 Jun 2020 18:39:49: Fewer paired peaks (574) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 574 pairs to build model! INFO @ Sun, 21 Jun 2020 18:39:49: start model_add_line... INFO @ Sun, 21 Jun 2020 18:39:49: start X-correlation... INFO @ Sun, 21 Jun 2020 18:39:49: end of X-cor INFO @ Sun, 21 Jun 2020 18:39:49: #2 finished! INFO @ Sun, 21 Jun 2020 18:39:49: #2 predicted fragment length is 62 bps INFO @ Sun, 21 Jun 2020 18:39:49: #2 alternative fragment length(s) may be 62,581 bps INFO @ Sun, 21 Jun 2020 18:39:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592480/SRX2592480.20_model.r WARNING @ Sun, 21 Jun 2020 18:39:49: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:39:49: #2 You may need to consider one of the other alternative d(s): 62,581 WARNING @ Sun, 21 Jun 2020 18:39:49: #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 18:39:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:39:49: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:40:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:40:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592480/SRX2592480.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:40:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592480/SRX2592480.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:40:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592480/SRX2592480.20_summits.bed INFO @ Sun, 21 Jun 2020 18:40:13: Done! pass1 - making usageList (100 chroms): 1 millis pass2 - checking and writing primary data (208 records, 4 fields): 5 millis CompletedMACS2peakCalling