Job ID = 16439004 SRX = SRX15206522 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: 00:05:18 14805375 reads; of these: 14805375 (100.00%) were unpaired; of these: 456986 (3.09%) aligned 0 times 11136626 (75.22%) aligned exactly 1 time 3211763 (21.69%) aligned >1 times 96.91% overall alignment rate Time searching: 00:05:18 Overall time: 00:05:18 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] 5658760 / 14348389 = 0.3944 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:31:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206522/SRX15206522.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206522/SRX15206522.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206522/SRX15206522.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206522/SRX15206522.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, 02 Aug 2022 14:31:59: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:31:59: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:32:05: 1000000 INFO @ Tue, 02 Aug 2022 14:32:11: 2000000 INFO @ Tue, 02 Aug 2022 14:32:17: 3000000 INFO @ Tue, 02 Aug 2022 14:32:23: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:32:29: 5000000 INFO @ Tue, 02 Aug 2022 14:32:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206522/SRX15206522.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206522/SRX15206522.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206522/SRX15206522.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206522/SRX15206522.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, 02 Aug 2022 14:32:29: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:32:29: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:32:36: 6000000 INFO @ Tue, 02 Aug 2022 14:32:36: 1000000 INFO @ Tue, 02 Aug 2022 14:32:43: 2000000 INFO @ Tue, 02 Aug 2022 14:32:43: 7000000 INFO @ Tue, 02 Aug 2022 14:32:50: 3000000 INFO @ Tue, 02 Aug 2022 14:32:50: 8000000 INFO @ Tue, 02 Aug 2022 14:32:55: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:32:55: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:32:55: #1 total tags in treatment: 8689629 INFO @ Tue, 02 Aug 2022 14:32:55: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:32:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:32:55: #1 tags after filtering in treatment: 8689490 INFO @ Tue, 02 Aug 2022 14:32:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:32:55: #1 finished! INFO @ Tue, 02 Aug 2022 14:32:55: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:32:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:32:56: #2 number of paired peaks: 1239 INFO @ Tue, 02 Aug 2022 14:32:56: start model_add_line... INFO @ Tue, 02 Aug 2022 14:32:56: start X-correlation... INFO @ Tue, 02 Aug 2022 14:32:56: end of X-cor INFO @ Tue, 02 Aug 2022 14:32:56: #2 finished! INFO @ Tue, 02 Aug 2022 14:32:56: #2 predicted fragment length is 117 bps INFO @ Tue, 02 Aug 2022 14:32:56: #2 alternative fragment length(s) may be 117 bps INFO @ Tue, 02 Aug 2022 14:32:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206522/SRX15206522.05_model.r WARNING @ Tue, 02 Aug 2022 14:32:56: #2 Since the d (117) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:32:56: #2 You may need to consider one of the other alternative d(s): 117 WARNING @ Tue, 02 Aug 2022 14:32:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:32:56: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:32:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:32:57: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:32:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206522/SRX15206522.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206522/SRX15206522.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206522/SRX15206522.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206522/SRX15206522.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, 02 Aug 2022 14:32:59: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:32:59: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:33:03: 5000000 INFO @ Tue, 02 Aug 2022 14:33:06: 1000000 INFO @ Tue, 02 Aug 2022 14:33:10: 6000000 INFO @ Tue, 02 Aug 2022 14:33:12: 2000000 INFO @ Tue, 02 Aug 2022 14:33:16: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:33:16: 7000000 INFO @ Tue, 02 Aug 2022 14:33:18: 3000000 INFO @ Tue, 02 Aug 2022 14:33:22: 8000000 INFO @ Tue, 02 Aug 2022 14:33:25: 4000000 INFO @ Tue, 02 Aug 2022 14:33:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206522/SRX15206522.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:33:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206522/SRX15206522.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:33:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206522/SRX15206522.05_summits.bed INFO @ Tue, 02 Aug 2022 14:33:26: Done! INFO @ Tue, 02 Aug 2022 14:33:27: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:33:27: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:33:27: #1 total tags in treatment: 8689629 INFO @ Tue, 02 Aug 2022 14:33:27: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:33:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:33:27: #1 tags after filtering in treatment: 8689490 INFO @ Tue, 02 Aug 2022 14:33:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:33:27: #1 finished! INFO @ Tue, 02 Aug 2022 14:33:27: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:33:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:33:28: #2 number of paired peaks: 1239 INFO @ Tue, 02 Aug 2022 14:33:28: start model_add_line... INFO @ Tue, 02 Aug 2022 14:33:28: start X-correlation... INFO @ Tue, 02 Aug 2022 14:33:28: end of X-cor INFO @ Tue, 02 Aug 2022 14:33:28: #2 finished! INFO @ Tue, 02 Aug 2022 14:33:28: #2 predicted fragment length is 117 bps INFO @ Tue, 02 Aug 2022 14:33:28: #2 alternative fragment length(s) may be 117 bps INFO @ Tue, 02 Aug 2022 14:33:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206522/SRX15206522.10_model.r WARNING @ Tue, 02 Aug 2022 14:33:28: #2 Since the d (117) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:33:28: #2 You may need to consider one of the other alternative d(s): 117 WARNING @ Tue, 02 Aug 2022 14:33:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:33:28: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:33:28: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (556 chroms): 1 millis pass2 - checking and writing primary data (3417 records, 4 fields): 42 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:33:31: 5000000 INFO @ Tue, 02 Aug 2022 14:33:37: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:33:43: 7000000 INFO @ Tue, 02 Aug 2022 14:33:48: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:33:49: 8000000 INFO @ Tue, 02 Aug 2022 14:33:53: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:33:53: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:33:53: #1 total tags in treatment: 8689629 INFO @ Tue, 02 Aug 2022 14:33:53: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:33:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:33:54: #1 tags after filtering in treatment: 8689490 INFO @ Tue, 02 Aug 2022 14:33:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:33:54: #1 finished! INFO @ Tue, 02 Aug 2022 14:33:54: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:33:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:33:54: #2 number of paired peaks: 1239 INFO @ Tue, 02 Aug 2022 14:33:54: start model_add_line... INFO @ Tue, 02 Aug 2022 14:33:54: start X-correlation... INFO @ Tue, 02 Aug 2022 14:33:54: end of X-cor INFO @ Tue, 02 Aug 2022 14:33:54: #2 finished! INFO @ Tue, 02 Aug 2022 14:33:54: #2 predicted fragment length is 117 bps INFO @ Tue, 02 Aug 2022 14:33:55: #2 alternative fragment length(s) may be 117 bps INFO @ Tue, 02 Aug 2022 14:33:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206522/SRX15206522.20_model.r WARNING @ Tue, 02 Aug 2022 14:33:55: #2 Since the d (117) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:33:55: #2 You may need to consider one of the other alternative d(s): 117 WARNING @ Tue, 02 Aug 2022 14:33:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:33:55: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:33:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:33:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206522/SRX15206522.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:33:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206522/SRX15206522.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:33:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206522/SRX15206522.10_summits.bed INFO @ Tue, 02 Aug 2022 14:33:58: Done! pass1 - making usageList (357 chroms): 1 millis pass2 - checking and writing primary data (1585 records, 4 fields): 19 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:34:15: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:34:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206522/SRX15206522.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:34:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206522/SRX15206522.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:34:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206522/SRX15206522.20_summits.bed INFO @ Tue, 02 Aug 2022 14:34:24: Done! pass1 - making usageList (197 chroms): 1 millis pass2 - checking and writing primary data (608 records, 4 fields): 18 millis CompletedMACS2peakCalling