Job ID = 16439167 SRX = SRX15206531 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: 00:22:04 19333458 reads; of these: 19333458 (100.00%) were unpaired; of these: 1583377 (8.19%) aligned 0 times 10727130 (55.48%) aligned exactly 1 time 7022951 (36.33%) aligned >1 times 91.81% overall alignment rate Time searching: 00:22:04 Overall time: 00:22:04 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 16 files... [bam_rmdupse_core] 10522471 / 17750081 = 0.5928 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 15:15:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206531/SRX15206531.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206531/SRX15206531.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206531/SRX15206531.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206531/SRX15206531.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 15:15:50: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:15:50: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:16:03: 1000000 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 15:16:17: 2000000 INFO @ Tue, 02 Aug 2022 15:16:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206531/SRX15206531.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206531/SRX15206531.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206531/SRX15206531.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206531/SRX15206531.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 15:16:18: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:16:18: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:16:31: 3000000 INFO @ Tue, 02 Aug 2022 15:16:32: 1000000 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 15:16:46: 4000000 INFO @ Tue, 02 Aug 2022 15:16:46: 2000000 INFO @ Tue, 02 Aug 2022 15:16:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206531/SRX15206531.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206531/SRX15206531.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206531/SRX15206531.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206531/SRX15206531.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 15:16:48: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:16:48: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:17:00: 3000000 INFO @ Tue, 02 Aug 2022 15:17:01: 5000000 INFO @ Tue, 02 Aug 2022 15:17:03: 1000000 INFO @ Tue, 02 Aug 2022 15:17:16: 4000000 INFO @ Tue, 02 Aug 2022 15:17:17: 2000000 INFO @ Tue, 02 Aug 2022 15:17:18: 6000000 INFO @ Tue, 02 Aug 2022 15:17:31: 5000000 INFO @ Tue, 02 Aug 2022 15:17:32: 3000000 INFO @ Tue, 02 Aug 2022 15:17:34: 7000000 INFO @ Tue, 02 Aug 2022 15:17:38: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 15:17:38: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 15:17:38: #1 total tags in treatment: 7227610 INFO @ Tue, 02 Aug 2022 15:17:38: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:17:38: #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 15:17:38: #1 tags after filtering in treatment: 7227468 INFO @ Tue, 02 Aug 2022 15:17:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:17:38: #1 finished! INFO @ Tue, 02 Aug 2022 15:17:38: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:17:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:17:39: #2 number of paired peaks: 4446 INFO @ Tue, 02 Aug 2022 15:17:39: start model_add_line... INFO @ Tue, 02 Aug 2022 15:17:39: start X-correlation... INFO @ Tue, 02 Aug 2022 15:17:39: end of X-cor INFO @ Tue, 02 Aug 2022 15:17:39: #2 finished! INFO @ Tue, 02 Aug 2022 15:17:39: #2 predicted fragment length is 193 bps INFO @ Tue, 02 Aug 2022 15:17:39: #2 alternative fragment length(s) may be 193 bps INFO @ Tue, 02 Aug 2022 15:17:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206531/SRX15206531.05_model.r WARNING @ Tue, 02 Aug 2022 15:17:40: #2 Since the d (193) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:17:40: #2 You may need to consider one of the other alternative d(s): 193 WARNING @ Tue, 02 Aug 2022 15:17:40: #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 15:17:40: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:17:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:17:45: 6000000 INFO @ Tue, 02 Aug 2022 15:17:46: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:18:00: 7000000 INFO @ Tue, 02 Aug 2022 15:18:02: 5000000 INFO @ Tue, 02 Aug 2022 15:18:03: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 15:18:03: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 15:18:03: #1 total tags in treatment: 7227610 INFO @ Tue, 02 Aug 2022 15:18:03: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:18:03: #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 15:18:03: #1 tags after filtering in treatment: 7227468 INFO @ Tue, 02 Aug 2022 15:18:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:18:03: #1 finished! INFO @ Tue, 02 Aug 2022 15:18:03: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:18:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:18:05: #2 number of paired peaks: 4446 INFO @ Tue, 02 Aug 2022 15:18:05: start model_add_line... INFO @ Tue, 02 Aug 2022 15:18:05: start X-correlation... INFO @ Tue, 02 Aug 2022 15:18:05: end of X-cor INFO @ Tue, 02 Aug 2022 15:18:05: #2 finished! INFO @ Tue, 02 Aug 2022 15:18:05: #2 predicted fragment length is 193 bps INFO @ Tue, 02 Aug 2022 15:18:05: #2 alternative fragment length(s) may be 193 bps INFO @ Tue, 02 Aug 2022 15:18:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206531/SRX15206531.10_model.r WARNING @ Tue, 02 Aug 2022 15:18:05: #2 Since the d (193) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:18:05: #2 You may need to consider one of the other alternative d(s): 193 WARNING @ Tue, 02 Aug 2022 15:18:05: #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 15:18:05: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:18:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:18:14: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:18:17: 6000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:18:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206531/SRX15206531.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:18:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206531/SRX15206531.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:18:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206531/SRX15206531.05_summits.bed INFO @ Tue, 02 Aug 2022 15:18:28: Done! pass1 - making usageList (618 chroms): 4 millis pass2 - checking and writing primary data (6252 records, 4 fields): 66 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:18:32: 7000000 INFO @ Tue, 02 Aug 2022 15:18:35: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 15:18:35: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 15:18:35: #1 total tags in treatment: 7227610 INFO @ Tue, 02 Aug 2022 15:18:35: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:18:35: #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 15:18:36: #1 tags after filtering in treatment: 7227468 INFO @ Tue, 02 Aug 2022 15:18:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:18:36: #1 finished! INFO @ Tue, 02 Aug 2022 15:18:36: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:18:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:18:37: #2 number of paired peaks: 4446 INFO @ Tue, 02 Aug 2022 15:18:37: start model_add_line... INFO @ Tue, 02 Aug 2022 15:18:37: start X-correlation... INFO @ Tue, 02 Aug 2022 15:18:37: end of X-cor INFO @ Tue, 02 Aug 2022 15:18:37: #2 finished! INFO @ Tue, 02 Aug 2022 15:18:37: #2 predicted fragment length is 193 bps INFO @ Tue, 02 Aug 2022 15:18:37: #2 alternative fragment length(s) may be 193 bps INFO @ Tue, 02 Aug 2022 15:18:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206531/SRX15206531.20_model.r WARNING @ Tue, 02 Aug 2022 15:18:37: #2 Since the d (193) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:18:37: #2 You may need to consider one of the other alternative d(s): 193 WARNING @ Tue, 02 Aug 2022 15:18:37: #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 15:18:37: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:18:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:18:39: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:18:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206531/SRX15206531.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:18:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206531/SRX15206531.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:18:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206531/SRX15206531.10_summits.bed INFO @ Tue, 02 Aug 2022 15:18:52: Done! pass1 - making usageList (487 chroms): 2 millis pass2 - checking and writing primary data (3552 records, 4 fields): 45 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:19:11: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:19:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206531/SRX15206531.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:19:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206531/SRX15206531.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:19:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206531/SRX15206531.20_summits.bed INFO @ Tue, 02 Aug 2022 15:19:25: Done! pass1 - making usageList (361 chroms): 2 millis pass2 - checking and writing primary data (1786 records, 4 fields): 28 millis CompletedMACS2peakCalling