Job ID = 16439154 SRX = SRX15206428 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: 00:07:43 17678586 reads; of these: 17678586 (100.00%) were unpaired; of these: 4060046 (22.97%) aligned 0 times 8162511 (46.17%) aligned exactly 1 time 5456029 (30.86%) aligned >1 times 77.03% overall alignment rate Time searching: 00:07:43 Overall time: 00:07:43 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] 5965682 / 13618540 = 0.4381 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 14:50:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206428/SRX15206428.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206428/SRX15206428.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206428/SRX15206428.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206428/SRX15206428.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 14:50:43: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:50:43: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:50:49: 1000000 INFO @ Tue, 02 Aug 2022 14:50:56: 2000000 INFO @ Tue, 02 Aug 2022 14:51:02: 3000000 INFO @ Tue, 02 Aug 2022 14:51:08: 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 14:51:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206428/SRX15206428.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206428/SRX15206428.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206428/SRX15206428.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206428/SRX15206428.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 14:51:13: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:51:13: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:51:15: 5000000 INFO @ Tue, 02 Aug 2022 14:51:20: 1000000 INFO @ Tue, 02 Aug 2022 14:51:23: 6000000 INFO @ Tue, 02 Aug 2022 14:51:27: 2000000 INFO @ Tue, 02 Aug 2022 14:51:30: 7000000 INFO @ Tue, 02 Aug 2022 14:51:34: 3000000 INFO @ Tue, 02 Aug 2022 14:51:35: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 14:51:35: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 14:51:35: #1 total tags in treatment: 7652858 INFO @ Tue, 02 Aug 2022 14:51:35: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:51:35: #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 14:51:36: #1 tags after filtering in treatment: 7652713 INFO @ Tue, 02 Aug 2022 14:51:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:51:36: #1 finished! INFO @ Tue, 02 Aug 2022 14:51:36: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:51:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:51:36: #2 number of paired peaks: 4964 INFO @ Tue, 02 Aug 2022 14:51:36: start model_add_line... INFO @ Tue, 02 Aug 2022 14:51:36: start X-correlation... INFO @ Tue, 02 Aug 2022 14:51:36: end of X-cor INFO @ Tue, 02 Aug 2022 14:51:36: #2 finished! INFO @ Tue, 02 Aug 2022 14:51:36: #2 predicted fragment length is 187 bps INFO @ Tue, 02 Aug 2022 14:51:36: #2 alternative fragment length(s) may be 187 bps INFO @ Tue, 02 Aug 2022 14:51:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206428/SRX15206428.05_model.r WARNING @ Tue, 02 Aug 2022 14:51:37: #2 Since the d (187) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:51:37: #2 You may need to consider one of the other alternative d(s): 187 WARNING @ Tue, 02 Aug 2022 14:51:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:51:37: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:51:37: #3 Pre-compute pvalue-qvalue table... 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 14:51:41: 4000000 INFO @ Tue, 02 Aug 2022 14:51:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206428/SRX15206428.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206428/SRX15206428.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206428/SRX15206428.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206428/SRX15206428.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 14:51:43: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:51:43: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:51:48: 5000000 INFO @ Tue, 02 Aug 2022 14:51:51: 1000000 INFO @ Tue, 02 Aug 2022 14:51:55: 6000000 INFO @ Tue, 02 Aug 2022 14:52:00: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:52:00: 2000000 INFO @ Tue, 02 Aug 2022 14:52:03: 7000000 INFO @ Tue, 02 Aug 2022 14:52:08: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 14:52:08: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 14:52:08: #1 total tags in treatment: 7652858 INFO @ Tue, 02 Aug 2022 14:52:08: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:52:08: #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 14:52:08: #1 tags after filtering in treatment: 7652713 INFO @ Tue, 02 Aug 2022 14:52:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:52:08: #1 finished! INFO @ Tue, 02 Aug 2022 14:52:08: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:52:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:52:08: 3000000 INFO @ Tue, 02 Aug 2022 14:52:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206428/SRX15206428.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:52:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206428/SRX15206428.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:52:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206428/SRX15206428.05_summits.bed INFO @ Tue, 02 Aug 2022 14:52:09: Done! INFO @ Tue, 02 Aug 2022 14:52:09: #2 number of paired peaks: 4964 INFO @ Tue, 02 Aug 2022 14:52:09: start model_add_line... INFO @ Tue, 02 Aug 2022 14:52:09: start X-correlation... INFO @ Tue, 02 Aug 2022 14:52:09: end of X-cor INFO @ Tue, 02 Aug 2022 14:52:09: #2 finished! INFO @ Tue, 02 Aug 2022 14:52:09: #2 predicted fragment length is 187 bps INFO @ Tue, 02 Aug 2022 14:52:09: #2 alternative fragment length(s) may be 187 bps INFO @ Tue, 02 Aug 2022 14:52:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206428/SRX15206428.10_model.r WARNING @ Tue, 02 Aug 2022 14:52:09: #2 Since the d (187) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:52:09: #2 You may need to consider one of the other alternative d(s): 187 WARNING @ Tue, 02 Aug 2022 14:52:09: #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 14:52:09: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:52:09: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (497 chroms): 1 millis pass2 - checking and writing primary data (4460 records, 4 fields): 43 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:52:16: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:52:24: 5000000 INFO @ Tue, 02 Aug 2022 14:52:32: 6000000 INFO @ Tue, 02 Aug 2022 14:52:32: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:52:40: 7000000 INFO @ Tue, 02 Aug 2022 14:52:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206428/SRX15206428.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:52:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206428/SRX15206428.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:52:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206428/SRX15206428.10_summits.bed INFO @ Tue, 02 Aug 2022 14:52:41: Done! pass1 - making usageList (438 chroms): 1 millis pass2 - checking and writing primary data (2806 records, 4 fields): 48 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:52:45: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 14:52:45: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 14:52:45: #1 total tags in treatment: 7652858 INFO @ Tue, 02 Aug 2022 14:52:45: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:52:45: #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 14:52:45: #1 tags after filtering in treatment: 7652713 INFO @ Tue, 02 Aug 2022 14:52:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:52:45: #1 finished! INFO @ Tue, 02 Aug 2022 14:52:45: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:52:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:52:46: #2 number of paired peaks: 4964 INFO @ Tue, 02 Aug 2022 14:52:46: start model_add_line... INFO @ Tue, 02 Aug 2022 14:52:46: start X-correlation... INFO @ Tue, 02 Aug 2022 14:52:46: end of X-cor INFO @ Tue, 02 Aug 2022 14:52:46: #2 finished! INFO @ Tue, 02 Aug 2022 14:52:46: #2 predicted fragment length is 187 bps INFO @ Tue, 02 Aug 2022 14:52:46: #2 alternative fragment length(s) may be 187 bps INFO @ Tue, 02 Aug 2022 14:52:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206428/SRX15206428.20_model.r WARNING @ Tue, 02 Aug 2022 14:52:46: #2 Since the d (187) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:52:46: #2 You may need to consider one of the other alternative d(s): 187 WARNING @ Tue, 02 Aug 2022 14:52:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:52:46: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:52:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:53:09: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:53:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206428/SRX15206428.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:53:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206428/SRX15206428.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:53:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206428/SRX15206428.20_summits.bed INFO @ Tue, 02 Aug 2022 14:53:18: Done! pass1 - making usageList (357 chroms): 1 millis pass2 - checking and writing primary data (1514 records, 4 fields): 29 millis CompletedMACS2peakCalling