Job ID = 14172418 SRX = SRX9427700 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: 00:07:42 19696958 reads; of these: 19696958 (100.00%) were unpaired; of these: 7875264 (39.98%) aligned 0 times 3170984 (16.10%) aligned exactly 1 time 8650710 (43.92%) aligned >1 times 60.02% overall alignment rate Time searching: 00:07:42 Overall time: 00:07:42 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] 4943589 / 11821694 = 0.4182 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 15:31:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9427700/SRX9427700.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9427700/SRX9427700.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9427700/SRX9427700.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9427700/SRX9427700.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 15:31:32: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:31:32: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:31:41: 1000000 INFO @ Sat, 11 Dec 2021 15:31:48: 2000000 INFO @ Sat, 11 Dec 2021 15:31:56: 3000000 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 15:32:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9427700/SRX9427700.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9427700/SRX9427700.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9427700/SRX9427700.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9427700/SRX9427700.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 15:32:02: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:32:02: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:32:05: 4000000 INFO @ Sat, 11 Dec 2021 15:32:14: 1000000 INFO @ Sat, 11 Dec 2021 15:32:15: 5000000 INFO @ Sat, 11 Dec 2021 15:32:23: 6000000 INFO @ Sat, 11 Dec 2021 15:32:27: 2000000 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 15:32:31: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 15:32:31: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 15:32:31: #1 total tags in treatment: 6878105 INFO @ Sat, 11 Dec 2021 15:32:31: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:32:31: #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 15:32:31: #1 tags after filtering in treatment: 6878094 INFO @ Sat, 11 Dec 2021 15:32:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 15:32:31: #1 finished! INFO @ Sat, 11 Dec 2021 15:32:31: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:32:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:32:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9427700/SRX9427700.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9427700/SRX9427700.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9427700/SRX9427700.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9427700/SRX9427700.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 15:32:32: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:32:32: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:32:33: #2 number of paired peaks: 6435 INFO @ Sat, 11 Dec 2021 15:32:33: start model_add_line... INFO @ Sat, 11 Dec 2021 15:32:33: start X-correlation... INFO @ Sat, 11 Dec 2021 15:32:33: end of X-cor INFO @ Sat, 11 Dec 2021 15:32:33: #2 finished! INFO @ Sat, 11 Dec 2021 15:32:33: #2 predicted fragment length is 59 bps INFO @ Sat, 11 Dec 2021 15:32:33: #2 alternative fragment length(s) may be 3,59 bps INFO @ Sat, 11 Dec 2021 15:32:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9427700/SRX9427700.05_model.r WARNING @ Sat, 11 Dec 2021 15:32:33: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:32:33: #2 You may need to consider one of the other alternative d(s): 3,59 WARNING @ Sat, 11 Dec 2021 15:32:33: #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 15:32:33: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:32:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:32:39: 3000000 INFO @ Sat, 11 Dec 2021 15:32:41: 1000000 INFO @ Sat, 11 Dec 2021 15:32:50: 2000000 INFO @ Sat, 11 Dec 2021 15:32:51: 4000000 INFO @ Sat, 11 Dec 2021 15:32:55: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:32:59: 3000000 INFO @ Sat, 11 Dec 2021 15:33:04: 5000000 INFO @ Sat, 11 Dec 2021 15:33:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9427700/SRX9427700.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:33:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9427700/SRX9427700.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:33:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9427700/SRX9427700.05_summits.bed INFO @ Sat, 11 Dec 2021 15:33:05: Done! pass1 - making usageList (1137 chroms): 4 millis pass2 - checking and writing primary data (5965 records, 4 fields): 57 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:33:08: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:33:16: 6000000 INFO @ Sat, 11 Dec 2021 15:33:17: 5000000 INFO @ Sat, 11 Dec 2021 15:33:26: 6000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 15:33:27: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 15:33:27: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 15:33:27: #1 total tags in treatment: 6878105 INFO @ Sat, 11 Dec 2021 15:33:27: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:33:27: #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 15:33:28: #1 tags after filtering in treatment: 6878094 INFO @ Sat, 11 Dec 2021 15:33:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 15:33:28: #1 finished! INFO @ Sat, 11 Dec 2021 15:33:28: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:33:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:33:29: #2 number of paired peaks: 6435 INFO @ Sat, 11 Dec 2021 15:33:29: start model_add_line... INFO @ Sat, 11 Dec 2021 15:33:29: start X-correlation... INFO @ Sat, 11 Dec 2021 15:33:29: end of X-cor INFO @ Sat, 11 Dec 2021 15:33:29: #2 finished! INFO @ Sat, 11 Dec 2021 15:33:29: #2 predicted fragment length is 59 bps INFO @ Sat, 11 Dec 2021 15:33:29: #2 alternative fragment length(s) may be 3,59 bps INFO @ Sat, 11 Dec 2021 15:33:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9427700/SRX9427700.10_model.r WARNING @ Sat, 11 Dec 2021 15:33:29: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:33:29: #2 You may need to consider one of the other alternative d(s): 3,59 WARNING @ Sat, 11 Dec 2021 15:33:29: #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 15:33:29: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:33:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:33:34: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 15:33:34: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 15:33:34: #1 total tags in treatment: 6878105 INFO @ Sat, 11 Dec 2021 15:33:34: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:33:34: #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 15:33:34: #1 tags after filtering in treatment: 6878094 INFO @ Sat, 11 Dec 2021 15:33:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 15:33:34: #1 finished! INFO @ Sat, 11 Dec 2021 15:33:34: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:33:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:33:35: #2 number of paired peaks: 6435 INFO @ Sat, 11 Dec 2021 15:33:35: start model_add_line... INFO @ Sat, 11 Dec 2021 15:33:35: start X-correlation... INFO @ Sat, 11 Dec 2021 15:33:36: end of X-cor INFO @ Sat, 11 Dec 2021 15:33:36: #2 finished! INFO @ Sat, 11 Dec 2021 15:33:36: #2 predicted fragment length is 59 bps INFO @ Sat, 11 Dec 2021 15:33:36: #2 alternative fragment length(s) may be 3,59 bps INFO @ Sat, 11 Dec 2021 15:33:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9427700/SRX9427700.20_model.r WARNING @ Sat, 11 Dec 2021 15:33:36: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:33:36: #2 You may need to consider one of the other alternative d(s): 3,59 WARNING @ Sat, 11 Dec 2021 15:33:36: #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 15:33:36: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:33:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:33:50: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:33:56: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:34:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9427700/SRX9427700.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:34:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9427700/SRX9427700.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:34:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9427700/SRX9427700.10_summits.bed INFO @ Sat, 11 Dec 2021 15:34:00: Done! pass1 - making usageList (971 chroms): 4 millis pass2 - checking and writing primary data (3353 records, 4 fields): 52 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:34:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9427700/SRX9427700.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:34:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9427700/SRX9427700.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:34:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9427700/SRX9427700.20_summits.bed INFO @ Sat, 11 Dec 2021 15:34:06: Done! pass1 - making usageList (567 chroms): 3 millis pass2 - checking and writing primary data (1518 records, 4 fields): 29 millis CompletedMACS2peakCalling