Job ID = 12266691 SRX = SRX8622126 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 2583034 spots for SRR12096686/SRR12096686.sra Written 2583034 spots for SRR12096686/SRR12096686.sra fastq に変換しました。 bowtie でマッピング中... Your job 12266838 ("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: 00:03:16 2583034 reads; of these: 2583034 (100.00%) were paired; of these: 2142989 (82.96%) aligned concordantly 0 times 357451 (13.84%) aligned concordantly exactly 1 time 82594 (3.20%) aligned concordantly >1 times ---- 2142989 pairs aligned concordantly 0 times; of these: 91812 (4.28%) aligned discordantly 1 time ---- 2051177 pairs aligned 0 times concordantly or discordantly; of these: 4102354 mates make up the pairs; of these: 4011787 (97.79%) aligned 0 times 28823 (0.70%) aligned exactly 1 time 61744 (1.51%) aligned >1 times 22.34% overall alignment rate Time searching: 00:03:16 Overall time: 00:03:16 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] 28792 / 525807 = 0.0548 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 09:10:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8622126/SRX8622126.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8622126/SRX8622126.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8622126/SRX8622126.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8622126/SRX8622126.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, 03 Apr 2021 09:10:24: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:10:24: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:10:33: 1000000 INFO @ Sat, 03 Apr 2021 09:10:33: #1 tag size is determined as 151 bps INFO @ Sat, 03 Apr 2021 09:10:33: #1 tag size = 151 INFO @ Sat, 03 Apr 2021 09:10:33: #1 total tags in treatment: 415592 INFO @ Sat, 03 Apr 2021 09:10:33: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:10:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 09:10:33: #1 tags after filtering in treatment: 407874 INFO @ Sat, 03 Apr 2021 09:10:33: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 03 Apr 2021 09:10:33: #1 finished! INFO @ Sat, 03 Apr 2021 09:10:33: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:10:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:10:34: #2 number of paired peaks: 2286 INFO @ Sat, 03 Apr 2021 09:10:34: start model_add_line... INFO @ Sat, 03 Apr 2021 09:10:34: start X-correlation... INFO @ Sat, 03 Apr 2021 09:10:34: end of X-cor INFO @ Sat, 03 Apr 2021 09:10:34: #2 finished! INFO @ Sat, 03 Apr 2021 09:10:34: #2 predicted fragment length is 219 bps INFO @ Sat, 03 Apr 2021 09:10:34: #2 alternative fragment length(s) may be 209,219 bps INFO @ Sat, 03 Apr 2021 09:10:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8622126/SRX8622126.05_model.r WARNING @ Sat, 03 Apr 2021 09:10:34: #2 Since the d (219) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:10:34: #2 You may need to consider one of the other alternative d(s): 209,219 WARNING @ Sat, 03 Apr 2021 09:10:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 09:10:34: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:10:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:10:35: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:10:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8622126/SRX8622126.05_peaks.xls INFO @ Sat, 03 Apr 2021 09:10:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8622126/SRX8622126.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:10:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8622126/SRX8622126.05_summits.bed INFO @ Sat, 03 Apr 2021 09:10:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (149 records, 4 fields): 1 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 09:10:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8622126/SRX8622126.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8622126/SRX8622126.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8622126/SRX8622126.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8622126/SRX8622126.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, 03 Apr 2021 09:10:54: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:10:54: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:11:04: 1000000 INFO @ Sat, 03 Apr 2021 09:11:05: #1 tag size is determined as 151 bps INFO @ Sat, 03 Apr 2021 09:11:05: #1 tag size = 151 INFO @ Sat, 03 Apr 2021 09:11:05: #1 total tags in treatment: 415592 INFO @ Sat, 03 Apr 2021 09:11:05: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:11:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 09:11:05: #1 tags after filtering in treatment: 407874 INFO @ Sat, 03 Apr 2021 09:11:05: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 03 Apr 2021 09:11:05: #1 finished! INFO @ Sat, 03 Apr 2021 09:11:05: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:11:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:11:05: #2 number of paired peaks: 2286 INFO @ Sat, 03 Apr 2021 09:11:05: start model_add_line... INFO @ Sat, 03 Apr 2021 09:11:05: start X-correlation... INFO @ Sat, 03 Apr 2021 09:11:05: end of X-cor INFO @ Sat, 03 Apr 2021 09:11:05: #2 finished! INFO @ Sat, 03 Apr 2021 09:11:05: #2 predicted fragment length is 219 bps INFO @ Sat, 03 Apr 2021 09:11:05: #2 alternative fragment length(s) may be 209,219 bps INFO @ Sat, 03 Apr 2021 09:11:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8622126/SRX8622126.10_model.r WARNING @ Sat, 03 Apr 2021 09:11:05: #2 Since the d (219) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:11:05: #2 You may need to consider one of the other alternative d(s): 209,219 WARNING @ Sat, 03 Apr 2021 09:11:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 09:11:05: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:11:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:11:06: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:11:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8622126/SRX8622126.10_peaks.xls INFO @ Sat, 03 Apr 2021 09:11:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8622126/SRX8622126.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:11:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8622126/SRX8622126.10_summits.bed INFO @ Sat, 03 Apr 2021 09:11:07: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (61 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 09:11:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8622126/SRX8622126.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8622126/SRX8622126.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8622126/SRX8622126.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8622126/SRX8622126.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, 03 Apr 2021 09:11:24: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:11:24: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 09:11:32: 1000000 INFO @ Sat, 03 Apr 2021 09:11:33: #1 tag size is determined as 151 bps INFO @ Sat, 03 Apr 2021 09:11:33: #1 tag size = 151 INFO @ Sat, 03 Apr 2021 09:11:33: #1 total tags in treatment: 415592 INFO @ Sat, 03 Apr 2021 09:11:33: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:11:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 09:11:33: #1 tags after filtering in treatment: 407874 INFO @ Sat, 03 Apr 2021 09:11:33: #1 Redundant rate of treatment: 0.02 INFO @ Sat, 03 Apr 2021 09:11:33: #1 finished! INFO @ Sat, 03 Apr 2021 09:11:33: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:11:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:11:33: #2 number of paired peaks: 2286 INFO @ Sat, 03 Apr 2021 09:11:33: start model_add_line... INFO @ Sat, 03 Apr 2021 09:11:33: start X-correlation... INFO @ Sat, 03 Apr 2021 09:11:33: end of X-cor INFO @ Sat, 03 Apr 2021 09:11:33: #2 finished! INFO @ Sat, 03 Apr 2021 09:11:33: #2 predicted fragment length is 219 bps INFO @ Sat, 03 Apr 2021 09:11:33: #2 alternative fragment length(s) may be 209,219 bps INFO @ Sat, 03 Apr 2021 09:11:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8622126/SRX8622126.20_model.r WARNING @ Sat, 03 Apr 2021 09:11:33: #2 Since the d (219) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:11:33: #2 You may need to consider one of the other alternative d(s): 209,219 WARNING @ Sat, 03 Apr 2021 09:11:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 09:11:33: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:11:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:11:34: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 09:11:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8622126/SRX8622126.20_peaks.xls INFO @ Sat, 03 Apr 2021 09:11:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8622126/SRX8622126.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:11:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8622126/SRX8622126.20_summits.bed INFO @ Sat, 03 Apr 2021 09:11:35: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (7 records, 4 fields): 3 millis CompletedMACS2peakCalling