Job ID = 6529740 SRX = SRX4669032 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:04:20 14031759 reads; of these: 14031759 (100.00%) were unpaired; of these: 522733 (3.73%) aligned 0 times 9037313 (64.41%) aligned exactly 1 time 4471713 (31.87%) aligned >1 times 96.27% overall alignment rate Time searching: 00:04:20 Overall time: 00:04:20 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] 3712387 / 13509026 = 0.2748 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 @ Tue, 30 Jun 2020 02:55:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669032/SRX4669032.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669032/SRX4669032.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669032/SRX4669032.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669032/SRX4669032.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 @ Tue, 30 Jun 2020 02:55:39: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:55:39: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:55:44: 1000000 INFO @ Tue, 30 Jun 2020 02:55:50: 2000000 INFO @ Tue, 30 Jun 2020 02:55:55: 3000000 INFO @ Tue, 30 Jun 2020 02:56:00: 4000000 INFO @ Tue, 30 Jun 2020 02:56:05: 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 @ Tue, 30 Jun 2020 02:56:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669032/SRX4669032.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669032/SRX4669032.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669032/SRX4669032.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669032/SRX4669032.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 @ Tue, 30 Jun 2020 02:56:09: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:56:09: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:56:11: 6000000 INFO @ Tue, 30 Jun 2020 02:56:16: 1000000 INFO @ Tue, 30 Jun 2020 02:56:17: 7000000 INFO @ Tue, 30 Jun 2020 02:56:23: 2000000 INFO @ Tue, 30 Jun 2020 02:56:23: 8000000 INFO @ Tue, 30 Jun 2020 02:56:29: 9000000 INFO @ Tue, 30 Jun 2020 02:56:30: 3000000 INFO @ Tue, 30 Jun 2020 02:56:34: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:56:34: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:56:34: #1 total tags in treatment: 9796639 INFO @ Tue, 30 Jun 2020 02:56:34: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:56:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:56:34: #1 tags after filtering in treatment: 9796622 INFO @ Tue, 30 Jun 2020 02:56:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:56:34: #1 finished! INFO @ Tue, 30 Jun 2020 02:56:34: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:56:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:56:35: #2 number of paired peaks: 487 WARNING @ Tue, 30 Jun 2020 02:56:35: Fewer paired peaks (487) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 487 pairs to build model! INFO @ Tue, 30 Jun 2020 02:56:35: start model_add_line... INFO @ Tue, 30 Jun 2020 02:56:35: start X-correlation... INFO @ Tue, 30 Jun 2020 02:56:35: end of X-cor INFO @ Tue, 30 Jun 2020 02:56:35: #2 finished! INFO @ Tue, 30 Jun 2020 02:56:35: #2 predicted fragment length is 75 bps INFO @ Tue, 30 Jun 2020 02:56:35: #2 alternative fragment length(s) may be 63,75 bps INFO @ Tue, 30 Jun 2020 02:56:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669032/SRX4669032.05_model.r WARNING @ Tue, 30 Jun 2020 02:56:35: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:56:35: #2 You may need to consider one of the other alternative d(s): 63,75 WARNING @ Tue, 30 Jun 2020 02:56:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:56:35: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:56:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:56:36: 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 @ Tue, 30 Jun 2020 02:56:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669032/SRX4669032.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669032/SRX4669032.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669032/SRX4669032.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669032/SRX4669032.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 @ Tue, 30 Jun 2020 02:56:39: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:56:39: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:56:43: 5000000 INFO @ Tue, 30 Jun 2020 02:56:45: 1000000 INFO @ Tue, 30 Jun 2020 02:56:50: 6000000 INFO @ Tue, 30 Jun 2020 02:56:51: 2000000 INFO @ Tue, 30 Jun 2020 02:56:57: 7000000 INFO @ Tue, 30 Jun 2020 02:56:57: 3000000 INFO @ Tue, 30 Jun 2020 02:56:58: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:57:03: 4000000 INFO @ Tue, 30 Jun 2020 02:57:04: 8000000 INFO @ Tue, 30 Jun 2020 02:57:09: 5000000 INFO @ Tue, 30 Jun 2020 02:57:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669032/SRX4669032.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:57:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669032/SRX4669032.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:57:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669032/SRX4669032.05_summits.bed INFO @ Tue, 30 Jun 2020 02:57:11: Done! INFO @ Tue, 30 Jun 2020 02:57:11: 9000000 pass1 - making usageList (769 chroms): 2 millis pass2 - checking and writing primary data (4122 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:57:14: 6000000 INFO @ Tue, 30 Jun 2020 02:57:16: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:57:16: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:57:16: #1 total tags in treatment: 9796639 INFO @ Tue, 30 Jun 2020 02:57:16: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:57:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:57:17: #1 tags after filtering in treatment: 9796622 INFO @ Tue, 30 Jun 2020 02:57:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:57:17: #1 finished! INFO @ Tue, 30 Jun 2020 02:57:17: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:57:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:57:18: #2 number of paired peaks: 487 WARNING @ Tue, 30 Jun 2020 02:57:18: Fewer paired peaks (487) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 487 pairs to build model! INFO @ Tue, 30 Jun 2020 02:57:18: start model_add_line... INFO @ Tue, 30 Jun 2020 02:57:18: start X-correlation... INFO @ Tue, 30 Jun 2020 02:57:18: end of X-cor INFO @ Tue, 30 Jun 2020 02:57:18: #2 finished! INFO @ Tue, 30 Jun 2020 02:57:18: #2 predicted fragment length is 75 bps INFO @ Tue, 30 Jun 2020 02:57:18: #2 alternative fragment length(s) may be 63,75 bps INFO @ Tue, 30 Jun 2020 02:57:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669032/SRX4669032.10_model.r WARNING @ Tue, 30 Jun 2020 02:57:18: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:57:18: #2 You may need to consider one of the other alternative d(s): 63,75 WARNING @ Tue, 30 Jun 2020 02:57:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:57:18: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:57:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:57:20: 7000000 INFO @ Tue, 30 Jun 2020 02:57:26: 8000000 INFO @ Tue, 30 Jun 2020 02:57:32: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:57:36: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:57:36: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:57:36: #1 total tags in treatment: 9796639 INFO @ Tue, 30 Jun 2020 02:57:36: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:57:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:57:37: #1 tags after filtering in treatment: 9796622 INFO @ Tue, 30 Jun 2020 02:57:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:57:37: #1 finished! INFO @ Tue, 30 Jun 2020 02:57:37: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:57:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:57:37: #2 number of paired peaks: 487 WARNING @ Tue, 30 Jun 2020 02:57:37: Fewer paired peaks (487) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 487 pairs to build model! INFO @ Tue, 30 Jun 2020 02:57:37: start model_add_line... INFO @ Tue, 30 Jun 2020 02:57:37: start X-correlation... INFO @ Tue, 30 Jun 2020 02:57:37: end of X-cor INFO @ Tue, 30 Jun 2020 02:57:37: #2 finished! INFO @ Tue, 30 Jun 2020 02:57:37: #2 predicted fragment length is 75 bps INFO @ Tue, 30 Jun 2020 02:57:37: #2 alternative fragment length(s) may be 63,75 bps INFO @ Tue, 30 Jun 2020 02:57:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669032/SRX4669032.20_model.r WARNING @ Tue, 30 Jun 2020 02:57:37: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:57:37: #2 You may need to consider one of the other alternative d(s): 63,75 WARNING @ Tue, 30 Jun 2020 02:57:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:57:37: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:57:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:57:40: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:57:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669032/SRX4669032.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:57:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669032/SRX4669032.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:57:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669032/SRX4669032.10_summits.bed INFO @ Tue, 30 Jun 2020 02:57:52: Done! pass1 - making usageList (559 chroms): 2 millis pass2 - checking and writing primary data (1520 records, 4 fields): 17 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:57:59: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:58:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669032/SRX4669032.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:58:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669032/SRX4669032.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:58:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669032/SRX4669032.20_summits.bed INFO @ Tue, 30 Jun 2020 02:58:11: Done! pass1 - making usageList (180 chroms): 1 millis pass2 - checking and writing primary data (306 records, 4 fields): 6 millis CompletedMACS2peakCalling