Job ID = 14170951 SRX = SRX9720883 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: 00:02:49 10206169 reads; of these: 10206169 (100.00%) were unpaired; of these: 577685 (5.66%) aligned 0 times 6501734 (63.70%) aligned exactly 1 time 3126750 (30.64%) aligned >1 times 94.34% overall alignment rate Time searching: 00:02:49 Overall time: 00:02:49 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] 1116674 / 9628484 = 0.1160 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 @ Sat, 11 Dec 2021 09:08:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9720883/SRX9720883.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9720883/SRX9720883.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9720883/SRX9720883.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9720883/SRX9720883.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 @ Sat, 11 Dec 2021 09:08:51: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:08:51: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:08:57: 1000000 INFO @ Sat, 11 Dec 2021 09:09:04: 2000000 INFO @ Sat, 11 Dec 2021 09:09:10: 3000000 INFO @ Sat, 11 Dec 2021 09:09:17: 4000000 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 @ Sat, 11 Dec 2021 09:09:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9720883/SRX9720883.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9720883/SRX9720883.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9720883/SRX9720883.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9720883/SRX9720883.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 @ Sat, 11 Dec 2021 09:09:21: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:09:21: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:09:24: 5000000 INFO @ Sat, 11 Dec 2021 09:09:28: 1000000 INFO @ Sat, 11 Dec 2021 09:09:31: 6000000 INFO @ Sat, 11 Dec 2021 09:09:35: 2000000 INFO @ Sat, 11 Dec 2021 09:09:38: 7000000 INFO @ Sat, 11 Dec 2021 09:09:41: 3000000 INFO @ Sat, 11 Dec 2021 09:09:46: 8000000 INFO @ Sat, 11 Dec 2021 09:09:48: 4000000 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 @ Sat, 11 Dec 2021 09:09:50: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:09:50: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:09:50: #1 total tags in treatment: 8511810 INFO @ Sat, 11 Dec 2021 09:09:50: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:09:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 09:09:51: #1 tags after filtering in treatment: 8511716 INFO @ Sat, 11 Dec 2021 09:09:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:09:51: #1 finished! INFO @ Sat, 11 Dec 2021 09:09:51: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:09:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:09:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9720883/SRX9720883.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9720883/SRX9720883.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9720883/SRX9720883.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9720883/SRX9720883.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 @ Sat, 11 Dec 2021 09:09:51: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:09:51: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:09:51: #2 number of paired peaks: 1488 INFO @ Sat, 11 Dec 2021 09:09:51: start model_add_line... INFO @ Sat, 11 Dec 2021 09:09:51: start X-correlation... INFO @ Sat, 11 Dec 2021 09:09:51: end of X-cor INFO @ Sat, 11 Dec 2021 09:09:51: #2 finished! INFO @ Sat, 11 Dec 2021 09:09:51: #2 predicted fragment length is 51 bps INFO @ Sat, 11 Dec 2021 09:09:51: #2 alternative fragment length(s) may be 3,51 bps INFO @ Sat, 11 Dec 2021 09:09:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9720883/SRX9720883.05_model.r WARNING @ Sat, 11 Dec 2021 09:09:51: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:09:51: #2 You may need to consider one of the other alternative d(s): 3,51 WARNING @ Sat, 11 Dec 2021 09:09:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 09:09:51: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:09:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:09:55: 5000000 INFO @ Sat, 11 Dec 2021 09:09:58: 1000000 INFO @ Sat, 11 Dec 2021 09:10:02: 6000000 INFO @ Sat, 11 Dec 2021 09:10:06: 2000000 INFO @ Sat, 11 Dec 2021 09:10:09: 7000000 INFO @ Sat, 11 Dec 2021 09:10:09: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:10:14: 3000000 INFO @ Sat, 11 Dec 2021 09:10:16: 8000000 INFO @ Sat, 11 Dec 2021 09:10:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9720883/SRX9720883.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:10:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9720883/SRX9720883.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:10:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9720883/SRX9720883.05_summits.bed INFO @ Sat, 11 Dec 2021 09:10:19: Done! INFO @ Sat, 11 Dec 2021 09:10:19: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:10:19: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:10:19: #1 total tags in treatment: 8511810 INFO @ Sat, 11 Dec 2021 09:10:19: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:10:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (581 chroms): 2 millis pass2 - checking and writing primary data (2488 records, 4 fields): 42 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:10:20: #1 tags after filtering in treatment: 8511716 INFO @ Sat, 11 Dec 2021 09:10:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:10:20: #1 finished! INFO @ Sat, 11 Dec 2021 09:10:20: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:10:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:10:20: #2 number of paired peaks: 1488 INFO @ Sat, 11 Dec 2021 09:10:20: start model_add_line... INFO @ Sat, 11 Dec 2021 09:10:20: start X-correlation... INFO @ Sat, 11 Dec 2021 09:10:20: end of X-cor INFO @ Sat, 11 Dec 2021 09:10:20: #2 finished! INFO @ Sat, 11 Dec 2021 09:10:20: #2 predicted fragment length is 51 bps INFO @ Sat, 11 Dec 2021 09:10:20: #2 alternative fragment length(s) may be 3,51 bps INFO @ Sat, 11 Dec 2021 09:10:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9720883/SRX9720883.10_model.r WARNING @ Sat, 11 Dec 2021 09:10:21: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:10:21: #2 You may need to consider one of the other alternative d(s): 3,51 WARNING @ Sat, 11 Dec 2021 09:10:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 09:10:21: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:10:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:10:21: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:10:28: 5000000 INFO @ Sat, 11 Dec 2021 09:10:35: 6000000 INFO @ Sat, 11 Dec 2021 09:10:38: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:10:42: 7000000 INFO @ Sat, 11 Dec 2021 09:10:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9720883/SRX9720883.10_peaks.xls BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:10:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9720883/SRX9720883.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:10:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9720883/SRX9720883.10_summits.bed INFO @ Sat, 11 Dec 2021 09:10:47: Done! pass1 - making usageList (460 chroms): 1 millis pass2 - checking and writing primary data (1430 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:10:49: 8000000 INFO @ Sat, 11 Dec 2021 09:10:53: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:10:53: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:10:53: #1 total tags in treatment: 8511810 INFO @ Sat, 11 Dec 2021 09:10:53: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:10:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 09:10:53: #1 tags after filtering in treatment: 8511716 INFO @ Sat, 11 Dec 2021 09:10:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:10:53: #1 finished! INFO @ Sat, 11 Dec 2021 09:10:53: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:10:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:10:54: #2 number of paired peaks: 1488 INFO @ Sat, 11 Dec 2021 09:10:54: start model_add_line... INFO @ Sat, 11 Dec 2021 09:10:54: start X-correlation... INFO @ Sat, 11 Dec 2021 09:10:54: end of X-cor INFO @ Sat, 11 Dec 2021 09:10:54: #2 finished! INFO @ Sat, 11 Dec 2021 09:10:54: #2 predicted fragment length is 51 bps INFO @ Sat, 11 Dec 2021 09:10:54: #2 alternative fragment length(s) may be 3,51 bps INFO @ Sat, 11 Dec 2021 09:10:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9720883/SRX9720883.20_model.r WARNING @ Sat, 11 Dec 2021 09:10:54: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:10:54: #2 You may need to consider one of the other alternative d(s): 3,51 WARNING @ Sat, 11 Dec 2021 09:10:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 09:10:54: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:10:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:11:11: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:11:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9720883/SRX9720883.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:11:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9720883/SRX9720883.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:11:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9720883/SRX9720883.20_summits.bed INFO @ Sat, 11 Dec 2021 09:11:20: Done! pass1 - making usageList (235 chroms): 1 millis pass2 - checking and writing primary data (502 records, 4 fields): 48 millis CompletedMACS2peakCalling