Job ID = 6452975 SRX = SRX084582 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:48:31 prefetch.2.10.7: 1) Downloading 'SRR315122'... 2020-06-21T07:48:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:53:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:53:46 prefetch.2.10.7: 1) 'SRR315122' was downloaded successfully Read 52414696 spots for SRR315122/SRR315122.sra Written 52414696 spots for SRR315122/SRR315122.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: 00:08:49 52414696 reads; of these: 52414696 (100.00%) were unpaired; of these: 18701556 (35.68%) aligned 0 times 23928557 (45.65%) aligned exactly 1 time 9784583 (18.67%) aligned >1 times 64.32% overall alignment rate Time searching: 00:08:49 Overall time: 00:08:49 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 12 files... [bam_rmdupse_core] 22579094 / 33713140 = 0.6697 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 17:10:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX084582/SRX084582.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX084582/SRX084582.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX084582/SRX084582.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX084582/SRX084582.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 17:10:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:10:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:10:08: 1000000 INFO @ Sun, 21 Jun 2020 17:10:13: 2000000 INFO @ Sun, 21 Jun 2020 17:10:17: 3000000 INFO @ Sun, 21 Jun 2020 17:10:22: 4000000 INFO @ Sun, 21 Jun 2020 17:10:27: 5000000 INFO @ Sun, 21 Jun 2020 17:10:32: 6000000 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 17:10:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX084582/SRX084582.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX084582/SRX084582.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX084582/SRX084582.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX084582/SRX084582.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 17:10:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:10:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:10:36: 7000000 INFO @ Sun, 21 Jun 2020 17:10:39: 1000000 INFO @ Sun, 21 Jun 2020 17:10:41: 8000000 INFO @ Sun, 21 Jun 2020 17:10:44: 2000000 INFO @ Sun, 21 Jun 2020 17:10:47: 9000000 INFO @ Sun, 21 Jun 2020 17:10:49: 3000000 INFO @ Sun, 21 Jun 2020 17:10:52: 10000000 INFO @ Sun, 21 Jun 2020 17:10:54: 4000000 INFO @ Sun, 21 Jun 2020 17:10:57: 11000000 INFO @ Sun, 21 Jun 2020 17:10:58: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:10:58: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:10:58: #1 total tags in treatment: 11134046 INFO @ Sun, 21 Jun 2020 17:10:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:10:58: #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 17:10:58: #1 tags after filtering in treatment: 11134007 INFO @ Sun, 21 Jun 2020 17:10:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:10:58: #1 finished! INFO @ Sun, 21 Jun 2020 17:10:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:10:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:10:59: 5000000 INFO @ Sun, 21 Jun 2020 17:11:00: #2 number of paired peaks: 4109 INFO @ Sun, 21 Jun 2020 17:11:00: start model_add_line... INFO @ Sun, 21 Jun 2020 17:11:00: start X-correlation... INFO @ Sun, 21 Jun 2020 17:11:00: end of X-cor INFO @ Sun, 21 Jun 2020 17:11:00: #2 finished! INFO @ Sun, 21 Jun 2020 17:11:00: #2 predicted fragment length is 69 bps INFO @ Sun, 21 Jun 2020 17:11:00: #2 alternative fragment length(s) may be 3,69 bps INFO @ Sun, 21 Jun 2020 17:11:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX084582/SRX084582.05_model.r WARNING @ Sun, 21 Jun 2020 17:11:00: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:11:00: #2 You may need to consider one of the other alternative d(s): 3,69 WARNING @ Sun, 21 Jun 2020 17:11:00: #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 17:11:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:11:00: #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 17:11:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX084582/SRX084582.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX084582/SRX084582.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX084582/SRX084582.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX084582/SRX084582.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 17:11:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:11:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:11:04: 6000000 INFO @ Sun, 21 Jun 2020 17:11:09: 1000000 INFO @ Sun, 21 Jun 2020 17:11:09: 7000000 INFO @ Sun, 21 Jun 2020 17:11:14: 8000000 INFO @ Sun, 21 Jun 2020 17:11:15: 2000000 INFO @ Sun, 21 Jun 2020 17:11:20: 9000000 INFO @ Sun, 21 Jun 2020 17:11:20: 3000000 INFO @ Sun, 21 Jun 2020 17:11:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:11:25: 10000000 INFO @ Sun, 21 Jun 2020 17:11:26: 4000000 INFO @ Sun, 21 Jun 2020 17:11:31: 11000000 INFO @ Sun, 21 Jun 2020 17:11:31: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:11:31: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:11:31: #1 total tags in treatment: 11134046 INFO @ Sun, 21 Jun 2020 17:11:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:11:31: #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 17:11:31: 5000000 INFO @ Sun, 21 Jun 2020 17:11:32: #1 tags after filtering in treatment: 11134007 INFO @ Sun, 21 Jun 2020 17:11:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:11:32: #1 finished! INFO @ Sun, 21 Jun 2020 17:11:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:11:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:11:33: #2 number of paired peaks: 4109 INFO @ Sun, 21 Jun 2020 17:11:33: start model_add_line... INFO @ Sun, 21 Jun 2020 17:11:33: start X-correlation... INFO @ Sun, 21 Jun 2020 17:11:33: end of X-cor INFO @ Sun, 21 Jun 2020 17:11:33: #2 finished! INFO @ Sun, 21 Jun 2020 17:11:33: #2 predicted fragment length is 69 bps INFO @ Sun, 21 Jun 2020 17:11:33: #2 alternative fragment length(s) may be 3,69 bps INFO @ Sun, 21 Jun 2020 17:11:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX084582/SRX084582.10_model.r WARNING @ Sun, 21 Jun 2020 17:11:33: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:11:33: #2 You may need to consider one of the other alternative d(s): 3,69 WARNING @ Sun, 21 Jun 2020 17:11:33: #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 17:11:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:11:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:11:37: 6000000 INFO @ Sun, 21 Jun 2020 17:11:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX084582/SRX084582.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:11:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX084582/SRX084582.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:11:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX084582/SRX084582.05_summits.bed INFO @ Sun, 21 Jun 2020 17:11:37: Done! pass1 - making usageList (835 chroms): 3 millis pass2 - checking and writing primary data (11897 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:11:42: 7000000 INFO @ Sun, 21 Jun 2020 17:11:48: 8000000 INFO @ Sun, 21 Jun 2020 17:11:53: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:11:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:11:59: 10000000 INFO @ Sun, 21 Jun 2020 17:12:04: 11000000 INFO @ Sun, 21 Jun 2020 17:12:05: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:12:05: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:12:05: #1 total tags in treatment: 11134046 INFO @ Sun, 21 Jun 2020 17:12:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:12:05: #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 17:12:05: #1 tags after filtering in treatment: 11134007 INFO @ Sun, 21 Jun 2020 17:12:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:12:05: #1 finished! INFO @ Sun, 21 Jun 2020 17:12:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:12:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:12:07: #2 number of paired peaks: 4109 INFO @ Sun, 21 Jun 2020 17:12:07: start model_add_line... INFO @ Sun, 21 Jun 2020 17:12:07: start X-correlation... INFO @ Sun, 21 Jun 2020 17:12:07: end of X-cor INFO @ Sun, 21 Jun 2020 17:12:07: #2 finished! INFO @ Sun, 21 Jun 2020 17:12:07: #2 predicted fragment length is 69 bps INFO @ Sun, 21 Jun 2020 17:12:07: #2 alternative fragment length(s) may be 3,69 bps INFO @ Sun, 21 Jun 2020 17:12:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX084582/SRX084582.20_model.r WARNING @ Sun, 21 Jun 2020 17:12:07: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:12:07: #2 You may need to consider one of the other alternative d(s): 3,69 WARNING @ Sun, 21 Jun 2020 17:12:07: #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 17:12:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:12:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:12:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX084582/SRX084582.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:12:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX084582/SRX084582.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:12:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX084582/SRX084582.10_summits.bed INFO @ Sun, 21 Jun 2020 17:12:10: Done! pass1 - making usageList (727 chroms): 2 millis pass2 - checking and writing primary data (7268 records, 4 fields): 24 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:12:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:12:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX084582/SRX084582.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:12:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX084582/SRX084582.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:12:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX084582/SRX084582.20_summits.bed INFO @ Sun, 21 Jun 2020 17:12:43: Done! pass1 - making usageList (571 chroms): 1 millis pass2 - checking and writing primary data (3646 records, 4 fields): 18 millis CompletedMACS2peakCalling