Job ID = 14167654 SRX = SRX4712963 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: 00:05:42 18470763 reads; of these: 18470763 (100.00%) were unpaired; of these: 530782 (2.87%) aligned 0 times 13184413 (71.38%) aligned exactly 1 time 4755568 (25.75%) aligned >1 times 97.13% overall alignment rate Time searching: 00:05:42 Overall time: 00:05:42 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] 2264735 / 17939981 = 0.1262 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 13:08:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4712963/SRX4712963.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4712963/SRX4712963.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4712963/SRX4712963.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4712963/SRX4712963.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 @ Fri, 10 Dec 2021 13:08:11: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:08:11: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:08:17: 1000000 INFO @ Fri, 10 Dec 2021 13:08:22: 2000000 INFO @ Fri, 10 Dec 2021 13:08:28: 3000000 INFO @ Fri, 10 Dec 2021 13:08:33: 4000000 INFO @ Fri, 10 Dec 2021 13:08:39: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 13:08:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4712963/SRX4712963.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4712963/SRX4712963.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4712963/SRX4712963.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4712963/SRX4712963.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 @ Fri, 10 Dec 2021 13:08:41: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:08:41: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:08:45: 6000000 INFO @ Fri, 10 Dec 2021 13:08:48: 1000000 INFO @ Fri, 10 Dec 2021 13:08:52: 7000000 INFO @ Fri, 10 Dec 2021 13:08:56: 2000000 INFO @ Fri, 10 Dec 2021 13:08:59: 8000000 INFO @ Fri, 10 Dec 2021 13:09:03: 3000000 INFO @ Fri, 10 Dec 2021 13:09:06: 9000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 13:09:10: 4000000 INFO @ Fri, 10 Dec 2021 13:09:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4712963/SRX4712963.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4712963/SRX4712963.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4712963/SRX4712963.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4712963/SRX4712963.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 @ Fri, 10 Dec 2021 13:09:11: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:09:11: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:09:12: 10000000 INFO @ Fri, 10 Dec 2021 13:09:16: 5000000 INFO @ Fri, 10 Dec 2021 13:09:18: 1000000 INFO @ Fri, 10 Dec 2021 13:09:19: 11000000 INFO @ Fri, 10 Dec 2021 13:09:23: 6000000 INFO @ Fri, 10 Dec 2021 13:09:25: 2000000 INFO @ Fri, 10 Dec 2021 13:09:26: 12000000 INFO @ Fri, 10 Dec 2021 13:09:30: 7000000 INFO @ Fri, 10 Dec 2021 13:09:31: 3000000 INFO @ Fri, 10 Dec 2021 13:09:33: 13000000 INFO @ Fri, 10 Dec 2021 13:09:37: 8000000 INFO @ Fri, 10 Dec 2021 13:09:38: 4000000 INFO @ Fri, 10 Dec 2021 13:09:39: 14000000 INFO @ Fri, 10 Dec 2021 13:09:44: 9000000 INFO @ Fri, 10 Dec 2021 13:09:44: 5000000 INFO @ Fri, 10 Dec 2021 13:09:46: 15000000 INFO @ Fri, 10 Dec 2021 13:09:51: 10000000 INFO @ Fri, 10 Dec 2021 13:09:51: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 13:09:51: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 13:09:51: #1 total tags in treatment: 15675246 INFO @ Fri, 10 Dec 2021 13:09:51: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:09:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 13:09:51: 6000000 INFO @ Fri, 10 Dec 2021 13:09:51: #1 tags after filtering in treatment: 15675238 INFO @ Fri, 10 Dec 2021 13:09:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:09:51: #1 finished! INFO @ Fri, 10 Dec 2021 13:09:51: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:09:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:09:52: #2 number of paired peaks: 468 WARNING @ Fri, 10 Dec 2021 13:09:52: Fewer paired peaks (468) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 468 pairs to build model! INFO @ Fri, 10 Dec 2021 13:09:52: start model_add_line... INFO @ Fri, 10 Dec 2021 13:09:52: start X-correlation... INFO @ Fri, 10 Dec 2021 13:09:52: end of X-cor INFO @ Fri, 10 Dec 2021 13:09:52: #2 finished! INFO @ Fri, 10 Dec 2021 13:09:52: #2 predicted fragment length is 59 bps INFO @ Fri, 10 Dec 2021 13:09:52: #2 alternative fragment length(s) may be 4,59 bps INFO @ Fri, 10 Dec 2021 13:09:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4712963/SRX4712963.05_model.r WARNING @ Fri, 10 Dec 2021 13:09:53: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:09:53: #2 You may need to consider one of the other alternative d(s): 4,59 WARNING @ Fri, 10 Dec 2021 13:09:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 13:09:53: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:09:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:09:57: 11000000 INFO @ Fri, 10 Dec 2021 13:09:57: 7000000 INFO @ Fri, 10 Dec 2021 13:10:04: 8000000 INFO @ Fri, 10 Dec 2021 13:10:04: 12000000 INFO @ Fri, 10 Dec 2021 13:10:10: 9000000 INFO @ Fri, 10 Dec 2021 13:10:11: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 13:10:17: 10000000 INFO @ Fri, 10 Dec 2021 13:10:18: 14000000 INFO @ Fri, 10 Dec 2021 13:10:21: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:10:24: 11000000 INFO @ Fri, 10 Dec 2021 13:10:25: 15000000 INFO @ Fri, 10 Dec 2021 13:10:30: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 13:10:30: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 13:10:30: #1 total tags in treatment: 15675246 INFO @ Fri, 10 Dec 2021 13:10:30: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:10:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 13:10:30: 12000000 INFO @ Fri, 10 Dec 2021 13:10:31: #1 tags after filtering in treatment: 15675238 INFO @ Fri, 10 Dec 2021 13:10:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:10:31: #1 finished! INFO @ Fri, 10 Dec 2021 13:10:31: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:10:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:10:32: #2 number of paired peaks: 468 WARNING @ Fri, 10 Dec 2021 13:10:32: Fewer paired peaks (468) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 468 pairs to build model! INFO @ Fri, 10 Dec 2021 13:10:32: start model_add_line... INFO @ Fri, 10 Dec 2021 13:10:32: start X-correlation... INFO @ Fri, 10 Dec 2021 13:10:32: end of X-cor INFO @ Fri, 10 Dec 2021 13:10:32: #2 finished! INFO @ Fri, 10 Dec 2021 13:10:32: #2 predicted fragment length is 59 bps INFO @ Fri, 10 Dec 2021 13:10:32: #2 alternative fragment length(s) may be 4,59 bps INFO @ Fri, 10 Dec 2021 13:10:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4712963/SRX4712963.10_model.r WARNING @ Fri, 10 Dec 2021 13:10:32: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:10:32: #2 You may need to consider one of the other alternative d(s): 4,59 WARNING @ Fri, 10 Dec 2021 13:10:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 13:10:32: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:10:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:10:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4712963/SRX4712963.05_peaks.xls INFO @ Fri, 10 Dec 2021 13:10:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4712963/SRX4712963.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:10:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4712963/SRX4712963.05_summits.bed INFO @ Fri, 10 Dec 2021 13:10:35: Done! pass1 - making usageList (518 chroms): 2 millis pass2 - checking and writing primary data (3386 records, 4 fields): 148 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 13:10:37: 13000000 INFO @ Fri, 10 Dec 2021 13:10:43: 14000000 INFO @ Fri, 10 Dec 2021 13:10:49: 15000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 13:10:53: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 13:10:53: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 13:10:53: #1 total tags in treatment: 15675246 INFO @ Fri, 10 Dec 2021 13:10:53: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:10:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 13:10:54: #1 tags after filtering in treatment: 15675238 INFO @ Fri, 10 Dec 2021 13:10:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:10:54: #1 finished! INFO @ Fri, 10 Dec 2021 13:10:54: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:10:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:10:55: #2 number of paired peaks: 468 WARNING @ Fri, 10 Dec 2021 13:10:55: Fewer paired peaks (468) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 468 pairs to build model! INFO @ Fri, 10 Dec 2021 13:10:55: start model_add_line... INFO @ Fri, 10 Dec 2021 13:10:55: start X-correlation... INFO @ Fri, 10 Dec 2021 13:10:55: end of X-cor INFO @ Fri, 10 Dec 2021 13:10:55: #2 finished! INFO @ Fri, 10 Dec 2021 13:10:55: #2 predicted fragment length is 59 bps INFO @ Fri, 10 Dec 2021 13:10:55: #2 alternative fragment length(s) may be 4,59 bps INFO @ Fri, 10 Dec 2021 13:10:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4712963/SRX4712963.20_model.r WARNING @ Fri, 10 Dec 2021 13:10:55: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:10:55: #2 You may need to consider one of the other alternative d(s): 4,59 WARNING @ Fri, 10 Dec 2021 13:10:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 13:10:55: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:10:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:11:03: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:11:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4712963/SRX4712963.10_peaks.xls INFO @ Fri, 10 Dec 2021 13:11:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4712963/SRX4712963.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:11:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4712963/SRX4712963.10_summits.bed INFO @ Fri, 10 Dec 2021 13:11:19: Done! pass1 - making usageList (379 chroms): 1 millis pass2 - checking and writing primary data (1373 records, 4 fields): 52 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 13:11:25: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:11:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4712963/SRX4712963.20_peaks.xls INFO @ Fri, 10 Dec 2021 13:11:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4712963/SRX4712963.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:11:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4712963/SRX4712963.20_summits.bed INFO @ Fri, 10 Dec 2021 13:11:39: Done! pass1 - making usageList (254 chroms): 1 millis pass2 - checking and writing primary data (590 records, 4 fields): 36 millis CompletedMACS2peakCalling