Job ID = 6509111 SRX = SRX647443 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T15:28:22 prefetch.2.10.7: 1) Downloading 'SRR1508426'... 2020-06-26T15:28:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T15:30:37 prefetch.2.10.7: HTTPS download succeed 2020-06-26T15:30:37 prefetch.2.10.7: 1) 'SRR1508426' was downloaded successfully Read 16994852 spots for SRR1508426/SRR1508426.sra Written 16994852 spots for SRR1508426/SRR1508426.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: 00:08:40 16994852 reads; of these: 16994852 (100.00%) were unpaired; of these: 5552993 (32.67%) aligned 0 times 8787814 (51.71%) aligned exactly 1 time 2654045 (15.62%) aligned >1 times 67.33% overall alignment rate Time searching: 00:08:40 Overall time: 00:08:40 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] 2482235 / 11441859 = 0.2169 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 @ Sat, 27 Jun 2020 00:45:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX647443/SRX647443.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX647443/SRX647443.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX647443/SRX647443.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX647443/SRX647443.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 @ Sat, 27 Jun 2020 00:45:30: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:45:30: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:45:37: 1000000 INFO @ Sat, 27 Jun 2020 00:45:44: 2000000 INFO @ Sat, 27 Jun 2020 00:45:51: 3000000 INFO @ Sat, 27 Jun 2020 00:45:58: 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 @ Sat, 27 Jun 2020 00:46:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX647443/SRX647443.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX647443/SRX647443.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX647443/SRX647443.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX647443/SRX647443.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 @ Sat, 27 Jun 2020 00:46:00: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:46:00: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:46:05: 5000000 INFO @ Sat, 27 Jun 2020 00:46:08: 1000000 INFO @ Sat, 27 Jun 2020 00:46:12: 6000000 INFO @ Sat, 27 Jun 2020 00:46:16: 2000000 INFO @ Sat, 27 Jun 2020 00:46:20: 7000000 INFO @ Sat, 27 Jun 2020 00:46:25: 3000000 INFO @ Sat, 27 Jun 2020 00:46:28: 8000000 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 @ Sat, 27 Jun 2020 00:46:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX647443/SRX647443.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX647443/SRX647443.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX647443/SRX647443.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX647443/SRX647443.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 @ Sat, 27 Jun 2020 00:46:30: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:46:30: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:46:33: 4000000 INFO @ Sat, 27 Jun 2020 00:46:35: #1 tag size is determined as 100 bps INFO @ Sat, 27 Jun 2020 00:46:35: #1 tag size = 100 INFO @ Sat, 27 Jun 2020 00:46:35: #1 total tags in treatment: 8959624 INFO @ Sat, 27 Jun 2020 00:46:35: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:46:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:46:36: #1 tags after filtering in treatment: 8959616 INFO @ Sat, 27 Jun 2020 00:46:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:46:36: #1 finished! INFO @ Sat, 27 Jun 2020 00:46:36: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:46:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:46:36: #2 number of paired peaks: 495 WARNING @ Sat, 27 Jun 2020 00:46:36: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Sat, 27 Jun 2020 00:46:36: start model_add_line... INFO @ Sat, 27 Jun 2020 00:46:37: start X-correlation... INFO @ Sat, 27 Jun 2020 00:46:37: end of X-cor INFO @ Sat, 27 Jun 2020 00:46:37: #2 finished! INFO @ Sat, 27 Jun 2020 00:46:37: #2 predicted fragment length is 110 bps INFO @ Sat, 27 Jun 2020 00:46:37: #2 alternative fragment length(s) may be 110 bps INFO @ Sat, 27 Jun 2020 00:46:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX647443/SRX647443.05_model.r WARNING @ Sat, 27 Jun 2020 00:46:37: #2 Since the d (110) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:46:37: #2 You may need to consider one of the other alternative d(s): 110 WARNING @ Sat, 27 Jun 2020 00:46:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:46:37: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:46:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:46:38: 1000000 INFO @ Sat, 27 Jun 2020 00:46:41: 5000000 INFO @ Sat, 27 Jun 2020 00:46:45: 2000000 INFO @ Sat, 27 Jun 2020 00:46:49: 6000000 INFO @ Sat, 27 Jun 2020 00:46:53: 3000000 INFO @ Sat, 27 Jun 2020 00:46:57: 7000000 INFO @ Sat, 27 Jun 2020 00:46:58: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:47:00: 4000000 INFO @ Sat, 27 Jun 2020 00:47:05: 8000000 INFO @ Sat, 27 Jun 2020 00:47:08: 5000000 INFO @ Sat, 27 Jun 2020 00:47:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX647443/SRX647443.05_peaks.xls INFO @ Sat, 27 Jun 2020 00:47:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX647443/SRX647443.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:47:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX647443/SRX647443.05_summits.bed INFO @ Sat, 27 Jun 2020 00:47:09: Done! pass1 - making usageList (506 chroms): 1 millis pass2 - checking and writing primary data (1500 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:47:13: #1 tag size is determined as 100 bps INFO @ Sat, 27 Jun 2020 00:47:13: #1 tag size = 100 INFO @ Sat, 27 Jun 2020 00:47:13: #1 total tags in treatment: 8959624 INFO @ Sat, 27 Jun 2020 00:47:13: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:47:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:47:14: #1 tags after filtering in treatment: 8959616 INFO @ Sat, 27 Jun 2020 00:47:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:47:14: #1 finished! INFO @ Sat, 27 Jun 2020 00:47:14: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:47:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:47:14: #2 number of paired peaks: 495 WARNING @ Sat, 27 Jun 2020 00:47:14: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Sat, 27 Jun 2020 00:47:14: start model_add_line... INFO @ Sat, 27 Jun 2020 00:47:14: start X-correlation... INFO @ Sat, 27 Jun 2020 00:47:14: end of X-cor INFO @ Sat, 27 Jun 2020 00:47:14: #2 finished! INFO @ Sat, 27 Jun 2020 00:47:14: #2 predicted fragment length is 110 bps INFO @ Sat, 27 Jun 2020 00:47:14: #2 alternative fragment length(s) may be 110 bps INFO @ Sat, 27 Jun 2020 00:47:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX647443/SRX647443.10_model.r WARNING @ Sat, 27 Jun 2020 00:47:14: #2 Since the d (110) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:47:14: #2 You may need to consider one of the other alternative d(s): 110 WARNING @ Sat, 27 Jun 2020 00:47:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:47:14: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:47:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:47:15: 6000000 INFO @ Sat, 27 Jun 2020 00:47:22: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 27 Jun 2020 00:47:29: 8000000 INFO @ Sat, 27 Jun 2020 00:47:35: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:47:36: #1 tag size is determined as 100 bps INFO @ Sat, 27 Jun 2020 00:47:36: #1 tag size = 100 INFO @ Sat, 27 Jun 2020 00:47:36: #1 total tags in treatment: 8959624 INFO @ Sat, 27 Jun 2020 00:47:36: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:47:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:47:36: #1 tags after filtering in treatment: 8959616 INFO @ Sat, 27 Jun 2020 00:47:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:47:36: #1 finished! INFO @ Sat, 27 Jun 2020 00:47:36: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:47:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:47:37: #2 number of paired peaks: 495 WARNING @ Sat, 27 Jun 2020 00:47:37: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Sat, 27 Jun 2020 00:47:37: start model_add_line... INFO @ Sat, 27 Jun 2020 00:47:37: start X-correlation... INFO @ Sat, 27 Jun 2020 00:47:37: end of X-cor INFO @ Sat, 27 Jun 2020 00:47:37: #2 finished! INFO @ Sat, 27 Jun 2020 00:47:37: #2 predicted fragment length is 110 bps INFO @ Sat, 27 Jun 2020 00:47:37: #2 alternative fragment length(s) may be 110 bps INFO @ Sat, 27 Jun 2020 00:47:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX647443/SRX647443.20_model.r WARNING @ Sat, 27 Jun 2020 00:47:37: #2 Since the d (110) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:47:37: #2 You may need to consider one of the other alternative d(s): 110 WARNING @ Sat, 27 Jun 2020 00:47:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:47:37: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:47:37: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 00:47:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX647443/SRX647443.10_peaks.xls INFO @ Sat, 27 Jun 2020 00:47:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX647443/SRX647443.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:47:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX647443/SRX647443.10_summits.bed INFO @ Sat, 27 Jun 2020 00:47:45: Done! pass1 - making usageList (310 chroms): 1 millis pass2 - checking and writing primary data (611 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:47:58: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:48:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX647443/SRX647443.20_peaks.xls INFO @ Sat, 27 Jun 2020 00:48:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX647443/SRX647443.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:48:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX647443/SRX647443.20_summits.bed INFO @ Sat, 27 Jun 2020 00:48:09: Done! pass1 - making usageList (156 chroms): 1 millis pass2 - checking and writing primary data (289 records, 4 fields): 7 millis CompletedMACS2peakCalling