Job ID = 14170225 SRX = SRX8556385 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 27358195 spots for SRR12024941/SRR12024941.sra Written 27358195 spots for SRR12024941/SRR12024941.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170714 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:37 27358195 reads; of these: 27358195 (100.00%) were paired; of these: 26132243 (95.52%) aligned concordantly 0 times 888006 (3.25%) aligned concordantly exactly 1 time 337946 (1.24%) aligned concordantly >1 times ---- 26132243 pairs aligned concordantly 0 times; of these: 180495 (0.69%) aligned discordantly 1 time ---- 25951748 pairs aligned 0 times concordantly or discordantly; of these: 51903496 mates make up the pairs; of these: 51456258 (99.14%) aligned 0 times 221184 (0.43%) aligned exactly 1 time 226054 (0.44%) aligned >1 times 5.96% overall alignment rate Time searching: 00:11:37 Overall time: 00:11:37 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 1021399 / 1384735 = 0.7376 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 06:06:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556385/SRX8556385.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556385/SRX8556385.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556385/SRX8556385.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556385/SRX8556385.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 06:06:42: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:06:42: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:06:51: 1000000 INFO @ Sat, 11 Dec 2021 06:06:52: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 06:06:52: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 06:06:52: #1 total tags in treatment: 313497 INFO @ Sat, 11 Dec 2021 06:06:52: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:06:52: #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 06:06:52: #1 tags after filtering in treatment: 264701 INFO @ Sat, 11 Dec 2021 06:06:52: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 11 Dec 2021 06:06:52: #1 finished! INFO @ Sat, 11 Dec 2021 06:06:52: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:06:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:06:52: #2 number of paired peaks: 3587 INFO @ Sat, 11 Dec 2021 06:06:52: start model_add_line... INFO @ Sat, 11 Dec 2021 06:06:52: start X-correlation... INFO @ Sat, 11 Dec 2021 06:06:53: end of X-cor INFO @ Sat, 11 Dec 2021 06:06:53: #2 finished! INFO @ Sat, 11 Dec 2021 06:06:53: #2 predicted fragment length is 167 bps INFO @ Sat, 11 Dec 2021 06:06:53: #2 alternative fragment length(s) may be 167 bps INFO @ Sat, 11 Dec 2021 06:06:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556385/SRX8556385.05_model.r WARNING @ Sat, 11 Dec 2021 06:06:53: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:06:53: #2 You may need to consider one of the other alternative d(s): 167 WARNING @ Sat, 11 Dec 2021 06:06:53: #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 06:06:53: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:06:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:06:53: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:06:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556385/SRX8556385.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:06:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556385/SRX8556385.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:06:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556385/SRX8556385.05_summits.bed INFO @ Sat, 11 Dec 2021 06:06:54: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (732 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 06:07:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556385/SRX8556385.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556385/SRX8556385.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556385/SRX8556385.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556385/SRX8556385.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 06:07:12: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:07:12: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:07:20: 1000000 INFO @ Sat, 11 Dec 2021 06:07:22: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 06:07:22: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 06:07:22: #1 total tags in treatment: 313497 INFO @ Sat, 11 Dec 2021 06:07:22: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:07:22: #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 06:07:22: #1 tags after filtering in treatment: 264701 INFO @ Sat, 11 Dec 2021 06:07:22: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 11 Dec 2021 06:07:22: #1 finished! INFO @ Sat, 11 Dec 2021 06:07:22: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:07:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:07:22: #2 number of paired peaks: 3587 INFO @ Sat, 11 Dec 2021 06:07:22: start model_add_line... INFO @ Sat, 11 Dec 2021 06:07:22: start X-correlation... INFO @ Sat, 11 Dec 2021 06:07:22: end of X-cor INFO @ Sat, 11 Dec 2021 06:07:22: #2 finished! INFO @ Sat, 11 Dec 2021 06:07:22: #2 predicted fragment length is 167 bps INFO @ Sat, 11 Dec 2021 06:07:22: #2 alternative fragment length(s) may be 167 bps INFO @ Sat, 11 Dec 2021 06:07:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556385/SRX8556385.10_model.r WARNING @ Sat, 11 Dec 2021 06:07:22: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:07:22: #2 You may need to consider one of the other alternative d(s): 167 WARNING @ Sat, 11 Dec 2021 06:07:22: #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 06:07:22: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:07:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:07:23: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:07:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556385/SRX8556385.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:07:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556385/SRX8556385.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:07:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556385/SRX8556385.10_summits.bed INFO @ Sat, 11 Dec 2021 06:07:23: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (431 records, 4 fields): 2 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 06:07:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556385/SRX8556385.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556385/SRX8556385.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556385/SRX8556385.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556385/SRX8556385.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 06:07:42: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:07:42: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:07:51: 1000000 INFO @ Sat, 11 Dec 2021 06:07:53: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 06:07:53: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 06:07:53: #1 total tags in treatment: 313497 INFO @ Sat, 11 Dec 2021 06:07:53: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:07:53: #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 06:07:53: #1 tags after filtering in treatment: 264701 INFO @ Sat, 11 Dec 2021 06:07:53: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 11 Dec 2021 06:07:53: #1 finished! INFO @ Sat, 11 Dec 2021 06:07:53: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:07:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:07:53: #2 number of paired peaks: 3587 INFO @ Sat, 11 Dec 2021 06:07:53: start model_add_line... INFO @ Sat, 11 Dec 2021 06:07:53: start X-correlation... INFO @ Sat, 11 Dec 2021 06:07:53: end of X-cor INFO @ Sat, 11 Dec 2021 06:07:53: #2 finished! INFO @ Sat, 11 Dec 2021 06:07:53: #2 predicted fragment length is 167 bps INFO @ Sat, 11 Dec 2021 06:07:53: #2 alternative fragment length(s) may be 167 bps INFO @ Sat, 11 Dec 2021 06:07:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556385/SRX8556385.20_model.r WARNING @ Sat, 11 Dec 2021 06:07:53: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:07:53: #2 You may need to consider one of the other alternative d(s): 167 WARNING @ Sat, 11 Dec 2021 06:07:53: #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 06:07:53: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:07:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:07:53: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:07:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556385/SRX8556385.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:07:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556385/SRX8556385.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:07:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556385/SRX8556385.20_summits.bed INFO @ Sat, 11 Dec 2021 06:07:54: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (206 records, 4 fields): 1 millis CompletedMACS2peakCalling