Job ID = 14168528 SRX = SRX8688960 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: 00:01:41 5418436 reads; of these: 5418436 (100.00%) were unpaired; of these: 664316 (12.26%) aligned 0 times 3426430 (63.24%) aligned exactly 1 time 1327690 (24.50%) aligned >1 times 87.74% overall alignment rate Time searching: 00:01:41 Overall time: 00:01:41 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_rmdupse_core] 363095 / 4754120 = 0.0764 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 18:57:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688960/SRX8688960.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688960/SRX8688960.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688960/SRX8688960.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688960/SRX8688960.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 18:57:31: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:57:31: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:57:37: 1000000 INFO @ Fri, 10 Dec 2021 18:57:43: 2000000 INFO @ Fri, 10 Dec 2021 18:57:48: 3000000 INFO @ Fri, 10 Dec 2021 18:57:54: 4000000 INFO @ Fri, 10 Dec 2021 18:57:57: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 18:57:57: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 18:57:57: #1 total tags in treatment: 4391025 INFO @ Fri, 10 Dec 2021 18:57:57: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:57:57: #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 18:57:57: #1 tags after filtering in treatment: 4390805 INFO @ Fri, 10 Dec 2021 18:57:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 18:57:57: #1 finished! INFO @ Fri, 10 Dec 2021 18:57:57: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:57:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:57:57: #2 number of paired peaks: 1071 INFO @ Fri, 10 Dec 2021 18:57:57: start model_add_line... INFO @ Fri, 10 Dec 2021 18:57:57: start X-correlation... INFO @ Fri, 10 Dec 2021 18:57:57: end of X-cor INFO @ Fri, 10 Dec 2021 18:57:57: #2 finished! INFO @ Fri, 10 Dec 2021 18:57:57: #2 predicted fragment length is 58 bps INFO @ Fri, 10 Dec 2021 18:57:57: #2 alternative fragment length(s) may be 58 bps INFO @ Fri, 10 Dec 2021 18:57:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688960/SRX8688960.05_model.r WARNING @ Fri, 10 Dec 2021 18:57:57: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:57:57: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Fri, 10 Dec 2021 18:57:57: #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 18:57:57: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:57:57: #3 Pre-compute pvalue-qvalue table... 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 18:58:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688960/SRX8688960.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688960/SRX8688960.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688960/SRX8688960.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688960/SRX8688960.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 18:58:01: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:58:01: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:58:07: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:58:07: 1000000 INFO @ Fri, 10 Dec 2021 18:58:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688960/SRX8688960.05_peaks.xls INFO @ Fri, 10 Dec 2021 18:58:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688960/SRX8688960.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:58:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688960/SRX8688960.05_summits.bed INFO @ Fri, 10 Dec 2021 18:58:11: Done! pass1 - making usageList (557 chroms): 3 millis pass2 - checking and writing primary data (1952 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 18:58:13: 2000000 INFO @ Fri, 10 Dec 2021 18:58:18: 3000000 INFO @ Fri, 10 Dec 2021 18:58:24: 4000000 INFO @ Fri, 10 Dec 2021 18:58:26: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 18:58:26: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 18:58:26: #1 total tags in treatment: 4391025 INFO @ Fri, 10 Dec 2021 18:58:26: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:58:26: #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 18:58:27: #1 tags after filtering in treatment: 4390805 INFO @ Fri, 10 Dec 2021 18:58:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 18:58:27: #1 finished! INFO @ Fri, 10 Dec 2021 18:58:27: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:58:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:58:27: #2 number of paired peaks: 1071 INFO @ Fri, 10 Dec 2021 18:58:27: start model_add_line... INFO @ Fri, 10 Dec 2021 18:58:27: start X-correlation... INFO @ Fri, 10 Dec 2021 18:58:27: end of X-cor INFO @ Fri, 10 Dec 2021 18:58:27: #2 finished! INFO @ Fri, 10 Dec 2021 18:58:27: #2 predicted fragment length is 58 bps INFO @ Fri, 10 Dec 2021 18:58:27: #2 alternative fragment length(s) may be 58 bps INFO @ Fri, 10 Dec 2021 18:58:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688960/SRX8688960.10_model.r WARNING @ Fri, 10 Dec 2021 18:58:27: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:58:27: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Fri, 10 Dec 2021 18:58:27: #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 18:58:27: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:58:27: #3 Pre-compute pvalue-qvalue table... 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 18:58:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688960/SRX8688960.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688960/SRX8688960.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688960/SRX8688960.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688960/SRX8688960.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 18:58:31: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:58:31: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:58:37: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:58:37: 1000000 INFO @ Fri, 10 Dec 2021 18:58:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688960/SRX8688960.10_peaks.xls INFO @ Fri, 10 Dec 2021 18:58:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688960/SRX8688960.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:58:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688960/SRX8688960.10_summits.bed INFO @ Fri, 10 Dec 2021 18:58:41: Done! pass1 - making usageList (401 chroms): 1 millis pass2 - checking and writing primary data (830 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 18:58:43: 2000000 INFO @ Fri, 10 Dec 2021 18:58:48: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 18:58:54: 4000000 INFO @ Fri, 10 Dec 2021 18:58:56: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 18:58:56: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 18:58:56: #1 total tags in treatment: 4391025 INFO @ Fri, 10 Dec 2021 18:58:56: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:58:56: #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 18:58:57: #1 tags after filtering in treatment: 4390805 INFO @ Fri, 10 Dec 2021 18:58:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 18:58:57: #1 finished! INFO @ Fri, 10 Dec 2021 18:58:57: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:58:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:58:57: #2 number of paired peaks: 1071 INFO @ Fri, 10 Dec 2021 18:58:57: start model_add_line... INFO @ Fri, 10 Dec 2021 18:58:57: start X-correlation... INFO @ Fri, 10 Dec 2021 18:58:57: end of X-cor INFO @ Fri, 10 Dec 2021 18:58:57: #2 finished! INFO @ Fri, 10 Dec 2021 18:58:57: #2 predicted fragment length is 58 bps INFO @ Fri, 10 Dec 2021 18:58:57: #2 alternative fragment length(s) may be 58 bps INFO @ Fri, 10 Dec 2021 18:58:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688960/SRX8688960.20_model.r WARNING @ Fri, 10 Dec 2021 18:58:57: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:58:57: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Fri, 10 Dec 2021 18:58:57: #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 18:58:57: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:58:57: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 18:59:07: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:59:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688960/SRX8688960.20_peaks.xls INFO @ Fri, 10 Dec 2021 18:59:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688960/SRX8688960.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:59:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688960/SRX8688960.20_summits.bed INFO @ Fri, 10 Dec 2021 18:59:12: Done! pass1 - making usageList (119 chroms): 0 millis pass2 - checking and writing primary data (207 records, 4 fields): 6 millis CompletedMACS2peakCalling