Job ID = 6530037 SRX = SRX6468501 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:12 25150510 reads; of these: 25150510 (100.00%) were unpaired; of these: 2642784 (10.51%) aligned 0 times 15589788 (61.99%) aligned exactly 1 time 6917938 (27.51%) aligned >1 times 89.49% overall alignment rate Time searching: 00:06:13 Overall time: 00:06:13 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] 11422475 / 22507726 = 0.5075 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 03:18:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6468501/SRX6468501.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6468501/SRX6468501.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6468501/SRX6468501.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6468501/SRX6468501.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 03:18:02: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:18:02: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:18:08: 1000000 INFO @ Tue, 30 Jun 2020 03:18:15: 2000000 INFO @ Tue, 30 Jun 2020 03:18:21: 3000000 INFO @ Tue, 30 Jun 2020 03:18:28: 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 @ Tue, 30 Jun 2020 03:18:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6468501/SRX6468501.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6468501/SRX6468501.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6468501/SRX6468501.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6468501/SRX6468501.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 03:18:32: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:18:32: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:18:36: 5000000 INFO @ Tue, 30 Jun 2020 03:18:38: 1000000 INFO @ Tue, 30 Jun 2020 03:18:42: 6000000 INFO @ Tue, 30 Jun 2020 03:18:45: 2000000 INFO @ Tue, 30 Jun 2020 03:18:49: 7000000 INFO @ Tue, 30 Jun 2020 03:18:51: 3000000 INFO @ Tue, 30 Jun 2020 03:18:55: 8000000 INFO @ Tue, 30 Jun 2020 03:18:57: 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 03:19:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6468501/SRX6468501.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6468501/SRX6468501.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6468501/SRX6468501.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6468501/SRX6468501.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 03:19:02: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:19:02: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:19:02: 9000000 INFO @ Tue, 30 Jun 2020 03:19:03: 5000000 INFO @ Tue, 30 Jun 2020 03:19:09: 10000000 INFO @ Tue, 30 Jun 2020 03:19:10: 6000000 INFO @ Tue, 30 Jun 2020 03:19:10: 1000000 INFO @ Tue, 30 Jun 2020 03:19:16: 11000000 INFO @ Tue, 30 Jun 2020 03:19:16: 7000000 INFO @ Tue, 30 Jun 2020 03:19:17: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:19:17: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:19:17: #1 total tags in treatment: 11085251 INFO @ Tue, 30 Jun 2020 03:19:17: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:19:17: #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 03:19:17: 2000000 INFO @ Tue, 30 Jun 2020 03:19:17: #1 tags after filtering in treatment: 11085250 INFO @ Tue, 30 Jun 2020 03:19:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:19:17: #1 finished! INFO @ Tue, 30 Jun 2020 03:19:17: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:19:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:19:18: #2 number of paired peaks: 526 WARNING @ Tue, 30 Jun 2020 03:19:18: Fewer paired peaks (526) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 526 pairs to build model! INFO @ Tue, 30 Jun 2020 03:19:18: start model_add_line... INFO @ Tue, 30 Jun 2020 03:19:18: start X-correlation... INFO @ Tue, 30 Jun 2020 03:19:18: end of X-cor INFO @ Tue, 30 Jun 2020 03:19:18: #2 finished! INFO @ Tue, 30 Jun 2020 03:19:18: #2 predicted fragment length is 39 bps INFO @ Tue, 30 Jun 2020 03:19:18: #2 alternative fragment length(s) may be 2,39,547,568 bps INFO @ Tue, 30 Jun 2020 03:19:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6468501/SRX6468501.05_model.r WARNING @ Tue, 30 Jun 2020 03:19:18: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:19:18: #2 You may need to consider one of the other alternative d(s): 2,39,547,568 WARNING @ Tue, 30 Jun 2020 03:19:18: #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 03:19:18: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:19:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:19:23: 8000000 INFO @ Tue, 30 Jun 2020 03:19:23: 3000000 INFO @ Tue, 30 Jun 2020 03:19:30: 9000000 INFO @ Tue, 30 Jun 2020 03:19:30: 4000000 INFO @ Tue, 30 Jun 2020 03:19:36: 10000000 INFO @ Tue, 30 Jun 2020 03:19:37: 5000000 INFO @ Tue, 30 Jun 2020 03:19:39: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:19:43: 11000000 INFO @ Tue, 30 Jun 2020 03:19:44: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:19:44: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:19:44: #1 total tags in treatment: 11085251 INFO @ Tue, 30 Jun 2020 03:19:44: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:19:44: #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 03:19:45: 6000000 INFO @ Tue, 30 Jun 2020 03:19:45: #1 tags after filtering in treatment: 11085250 INFO @ Tue, 30 Jun 2020 03:19:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:19:45: #1 finished! INFO @ Tue, 30 Jun 2020 03:19:45: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:19:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:19:45: #2 number of paired peaks: 526 WARNING @ Tue, 30 Jun 2020 03:19:45: Fewer paired peaks (526) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 526 pairs to build model! INFO @ Tue, 30 Jun 2020 03:19:45: start model_add_line... INFO @ Tue, 30 Jun 2020 03:19:46: start X-correlation... INFO @ Tue, 30 Jun 2020 03:19:46: end of X-cor INFO @ Tue, 30 Jun 2020 03:19:46: #2 finished! INFO @ Tue, 30 Jun 2020 03:19:46: #2 predicted fragment length is 39 bps INFO @ Tue, 30 Jun 2020 03:19:46: #2 alternative fragment length(s) may be 2,39,547,568 bps INFO @ Tue, 30 Jun 2020 03:19:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6468501/SRX6468501.10_model.r WARNING @ Tue, 30 Jun 2020 03:19:46: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:19:46: #2 You may need to consider one of the other alternative d(s): 2,39,547,568 WARNING @ Tue, 30 Jun 2020 03:19:46: #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 03:19:46: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:19:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:19:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6468501/SRX6468501.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:19:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6468501/SRX6468501.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:19:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6468501/SRX6468501.05_summits.bed INFO @ Tue, 30 Jun 2020 03:19:50: Done! pass1 - making usageList (590 chroms): 2 millis pass2 - checking and writing primary data (2232 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:19:51: 7000000 INFO @ Tue, 30 Jun 2020 03:19:57: 8000000 INFO @ Tue, 30 Jun 2020 03:20:05: 9000000 INFO @ Tue, 30 Jun 2020 03:20:06: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:20:12: 10000000 INFO @ Tue, 30 Jun 2020 03:20:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6468501/SRX6468501.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:20:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6468501/SRX6468501.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:20:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6468501/SRX6468501.10_summits.bed INFO @ Tue, 30 Jun 2020 03:20:17: Done! pass1 - making usageList (427 chroms): 2 millis pass2 - checking and writing primary data (1551 records, 4 fields): 135 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:20:18: 11000000 INFO @ Tue, 30 Jun 2020 03:20:19: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:20:19: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:20:19: #1 total tags in treatment: 11085251 INFO @ Tue, 30 Jun 2020 03:20:19: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:20:19: #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 03:20:20: #1 tags after filtering in treatment: 11085250 INFO @ Tue, 30 Jun 2020 03:20:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:20:20: #1 finished! INFO @ Tue, 30 Jun 2020 03:20:20: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:20:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:20:21: #2 number of paired peaks: 526 WARNING @ Tue, 30 Jun 2020 03:20:21: Fewer paired peaks (526) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 526 pairs to build model! INFO @ Tue, 30 Jun 2020 03:20:21: start model_add_line... INFO @ Tue, 30 Jun 2020 03:20:21: start X-correlation... INFO @ Tue, 30 Jun 2020 03:20:21: end of X-cor INFO @ Tue, 30 Jun 2020 03:20:21: #2 finished! INFO @ Tue, 30 Jun 2020 03:20:21: #2 predicted fragment length is 39 bps INFO @ Tue, 30 Jun 2020 03:20:21: #2 alternative fragment length(s) may be 2,39,547,568 bps INFO @ Tue, 30 Jun 2020 03:20:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6468501/SRX6468501.20_model.r WARNING @ Tue, 30 Jun 2020 03:20:21: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:20:21: #2 You may need to consider one of the other alternative d(s): 2,39,547,568 WARNING @ Tue, 30 Jun 2020 03:20:21: #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 03:20:21: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:20:21: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:20:42: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:20:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6468501/SRX6468501.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:20:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6468501/SRX6468501.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:20:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6468501/SRX6468501.20_summits.bed INFO @ Tue, 30 Jun 2020 03:20:53: Done! pass1 - making usageList (144 chroms): 1 millis pass2 - checking and writing primary data (262 records, 4 fields): 9 millis CompletedMACS2peakCalling