Job ID = 14171514 SRX = SRX10000682 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: 00:09:48 46746110 reads; of these: 46746110 (100.00%) were unpaired; of these: 44528554 (95.26%) aligned 0 times 1826214 (3.91%) aligned exactly 1 time 391342 (0.84%) aligned >1 times 4.74% overall alignment rate Time searching: 00:09:49 Overall time: 00:09:49 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] 259287 / 2217556 = 0.1169 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 12:04:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10000682/SRX10000682.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10000682/SRX10000682.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10000682/SRX10000682.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10000682/SRX10000682.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 12:04:13: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:04:13: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:04:23: 1000000 INFO @ Sat, 11 Dec 2021 12:04:35: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 12:04:35: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 12:04:35: #1 total tags in treatment: 1958269 INFO @ Sat, 11 Dec 2021 12:04:35: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:04:35: #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 12:04:35: #1 tags after filtering in treatment: 1957876 INFO @ Sat, 11 Dec 2021 12:04:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 12:04:35: #1 finished! INFO @ Sat, 11 Dec 2021 12:04:35: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:04:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:04:35: #2 number of paired peaks: 1704 INFO @ Sat, 11 Dec 2021 12:04:35: start model_add_line... INFO @ Sat, 11 Dec 2021 12:04:35: start X-correlation... INFO @ Sat, 11 Dec 2021 12:04:35: end of X-cor INFO @ Sat, 11 Dec 2021 12:04:35: #2 finished! INFO @ Sat, 11 Dec 2021 12:04:35: #2 predicted fragment length is 114 bps INFO @ Sat, 11 Dec 2021 12:04:35: #2 alternative fragment length(s) may be 114 bps INFO @ Sat, 11 Dec 2021 12:04:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10000682/SRX10000682.05_model.r WARNING @ Sat, 11 Dec 2021 12:04:35: #2 Since the d (114) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:04:35: #2 You may need to consider one of the other alternative d(s): 114 WARNING @ Sat, 11 Dec 2021 12:04:35: #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 12:04:35: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:04:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:04:40: #3 Call peaks for each chromosome... 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 12:04:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10000682/SRX10000682.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10000682/SRX10000682.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10000682/SRX10000682.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10000682/SRX10000682.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 12:04:43: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:04:43: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:04:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10000682/SRX10000682.05_peaks.xls INFO @ Sat, 11 Dec 2021 12:04:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10000682/SRX10000682.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:04:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10000682/SRX10000682.05_summits.bed INFO @ Sat, 11 Dec 2021 12:04:43: Done! pass1 - making usageList (112 chroms): 1 millis pass2 - checking and writing primary data (359 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 12:04:51: 1000000 INFO @ Sat, 11 Dec 2021 12:04:59: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 12:04:59: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 12:04:59: #1 total tags in treatment: 1958269 INFO @ Sat, 11 Dec 2021 12:04:59: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:04:59: #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 12:04:59: #1 tags after filtering in treatment: 1957876 INFO @ Sat, 11 Dec 2021 12:04:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 12:04:59: #1 finished! INFO @ Sat, 11 Dec 2021 12:04:59: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:04:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:05:00: #2 number of paired peaks: 1704 INFO @ Sat, 11 Dec 2021 12:05:00: start model_add_line... INFO @ Sat, 11 Dec 2021 12:05:00: start X-correlation... INFO @ Sat, 11 Dec 2021 12:05:00: end of X-cor INFO @ Sat, 11 Dec 2021 12:05:00: #2 finished! INFO @ Sat, 11 Dec 2021 12:05:00: #2 predicted fragment length is 114 bps INFO @ Sat, 11 Dec 2021 12:05:00: #2 alternative fragment length(s) may be 114 bps INFO @ Sat, 11 Dec 2021 12:05:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10000682/SRX10000682.10_model.r WARNING @ Sat, 11 Dec 2021 12:05:00: #2 Since the d (114) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:05:00: #2 You may need to consider one of the other alternative d(s): 114 WARNING @ Sat, 11 Dec 2021 12:05:00: #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 12:05:00: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:05:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 12:05:04: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:05:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10000682/SRX10000682.10_peaks.xls INFO @ Sat, 11 Dec 2021 12:05:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10000682/SRX10000682.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:05:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10000682/SRX10000682.10_summits.bed INFO @ Sat, 11 Dec 2021 12:05:07: Done! pass1 - making usageList (71 chroms): 1 millis pass2 - checking and writing primary data (164 records, 4 fields): 7 millis CompletedMACS2peakCalling 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 12:05:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10000682/SRX10000682.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10000682/SRX10000682.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10000682/SRX10000682.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10000682/SRX10000682.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 12:05:13: #1 read tag files... INFO @ Sat, 11 Dec 2021 12:05:13: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 12:05:21: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 12:05:30: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 12:05:30: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 12:05:30: #1 total tags in treatment: 1958269 INFO @ Sat, 11 Dec 2021 12:05:30: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 12:05:30: #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 12:05:30: #1 tags after filtering in treatment: 1957876 INFO @ Sat, 11 Dec 2021 12:05:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 12:05:30: #1 finished! INFO @ Sat, 11 Dec 2021 12:05:30: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 12:05:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 12:05:30: #2 number of paired peaks: 1704 INFO @ Sat, 11 Dec 2021 12:05:30: start model_add_line... INFO @ Sat, 11 Dec 2021 12:05:30: start X-correlation... INFO @ Sat, 11 Dec 2021 12:05:30: end of X-cor INFO @ Sat, 11 Dec 2021 12:05:30: #2 finished! INFO @ Sat, 11 Dec 2021 12:05:30: #2 predicted fragment length is 114 bps INFO @ Sat, 11 Dec 2021 12:05:30: #2 alternative fragment length(s) may be 114 bps INFO @ Sat, 11 Dec 2021 12:05:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10000682/SRX10000682.20_model.r WARNING @ Sat, 11 Dec 2021 12:05:31: #2 Since the d (114) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 12:05:31: #2 You may need to consider one of the other alternative d(s): 114 WARNING @ Sat, 11 Dec 2021 12:05:31: #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 12:05:31: #3 Call peaks... INFO @ Sat, 11 Dec 2021 12:05:31: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 12:05:35: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 12:05:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10000682/SRX10000682.20_peaks.xls INFO @ Sat, 11 Dec 2021 12:05:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10000682/SRX10000682.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 12:05:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10000682/SRX10000682.20_summits.bed INFO @ Sat, 11 Dec 2021 12:05:38: Done! pass1 - making usageList (43 chroms): 1 millis pass2 - checking and writing primary data (76 records, 4 fields): 5 millis CompletedMACS2peakCalling