Job ID = 14171223 SRX = SRX9555335 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 2558427 spots for SRR13110845/SRR13110845.sra Written 2558427 spots for SRR13110845/SRR13110845.sra Read 2392509 spots for SRR13110846/SRR13110846.sra Written 2392509 spots for SRR13110846/SRR13110846.sra Read 2405247 spots for SRR13110847/SRR13110847.sra Written 2405247 spots for SRR13110847/SRR13110847.sra Read 2303001 spots for SRR13110848/SRR13110848.sra Written 2303001 spots for SRR13110848/SRR13110848.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171683 ("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: 00:02:46 9659184 reads; of these: 9659184 (100.00%) were paired; of these: 9375931 (97.07%) aligned concordantly 0 times 196441 (2.03%) aligned concordantly exactly 1 time 86812 (0.90%) aligned concordantly >1 times ---- 9375931 pairs aligned concordantly 0 times; of these: 2058 (0.02%) aligned discordantly 1 time ---- 9373873 pairs aligned 0 times concordantly or discordantly; of these: 18747746 mates make up the pairs; of these: 18718154 (99.84%) aligned 0 times 8701 (0.05%) aligned exactly 1 time 20891 (0.11%) aligned >1 times 3.11% overall alignment rate Time searching: 00:02:47 Overall time: 00:02:47 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] 2151 / 85775 = 0.0251 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 10:40:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555335/SRX9555335.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555335/SRX9555335.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555335/SRX9555335.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555335/SRX9555335.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 10:40:57: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:40:57: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:41:06: #1 tag size is determined as 60 bps INFO @ Sat, 11 Dec 2021 10:41:06: #1 tag size = 60 INFO @ Sat, 11 Dec 2021 10:41:06: #1 total tags in treatment: 281105 INFO @ Sat, 11 Dec 2021 10:41:06: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:41:06: #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 10:41:06: #1 tags after filtering in treatment: 272971 INFO @ Sat, 11 Dec 2021 10:41:06: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 10:41:06: #1 finished! INFO @ Sat, 11 Dec 2021 10:41:06: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:41:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:41:06: #2 number of paired peaks: 1513 INFO @ Sat, 11 Dec 2021 10:41:06: start model_add_line... INFO @ Sat, 11 Dec 2021 10:41:06: start X-correlation... INFO @ Sat, 11 Dec 2021 10:41:06: end of X-cor INFO @ Sat, 11 Dec 2021 10:41:06: #2 finished! INFO @ Sat, 11 Dec 2021 10:41:06: #2 predicted fragment length is 47 bps INFO @ Sat, 11 Dec 2021 10:41:06: #2 alternative fragment length(s) may be 47,492,562 bps INFO @ Sat, 11 Dec 2021 10:41:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555335/SRX9555335.05_model.r WARNING @ Sat, 11 Dec 2021 10:41:06: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 10:41:06: #2 You may need to consider one of the other alternative d(s): 47,492,562 WARNING @ Sat, 11 Dec 2021 10:41:06: #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 10:41:06: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:41:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:41:07: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:41:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555335/SRX9555335.05_peaks.xls INFO @ Sat, 11 Dec 2021 10:41:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555335/SRX9555335.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:41:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555335/SRX9555335.05_summits.bed INFO @ Sat, 11 Dec 2021 10:41:07: Done! pass1 - making usageList (8 chroms): 2 millis pass2 - checking and writing primary data (172 records, 4 fields): 30 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 10:41:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555335/SRX9555335.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555335/SRX9555335.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555335/SRX9555335.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555335/SRX9555335.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 10:41:26: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:41:26: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:41:34: #1 tag size is determined as 60 bps INFO @ Sat, 11 Dec 2021 10:41:34: #1 tag size = 60 INFO @ Sat, 11 Dec 2021 10:41:34: #1 total tags in treatment: 281105 INFO @ Sat, 11 Dec 2021 10:41:34: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:41:34: #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 10:41:34: #1 tags after filtering in treatment: 272971 INFO @ Sat, 11 Dec 2021 10:41:34: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 10:41:34: #1 finished! INFO @ Sat, 11 Dec 2021 10:41:34: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:41:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:41:34: #2 number of paired peaks: 1513 INFO @ Sat, 11 Dec 2021 10:41:34: start model_add_line... INFO @ Sat, 11 Dec 2021 10:41:34: start X-correlation... INFO @ Sat, 11 Dec 2021 10:41:34: end of X-cor INFO @ Sat, 11 Dec 2021 10:41:34: #2 finished! INFO @ Sat, 11 Dec 2021 10:41:34: #2 predicted fragment length is 47 bps INFO @ Sat, 11 Dec 2021 10:41:34: #2 alternative fragment length(s) may be 47,492,562 bps INFO @ Sat, 11 Dec 2021 10:41:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555335/SRX9555335.10_model.r WARNING @ Sat, 11 Dec 2021 10:41:34: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 10:41:34: #2 You may need to consider one of the other alternative d(s): 47,492,562 WARNING @ Sat, 11 Dec 2021 10:41:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 10:41:34: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:41:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:41:35: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:41:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555335/SRX9555335.10_peaks.xls INFO @ Sat, 11 Dec 2021 10:41:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555335/SRX9555335.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:41:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555335/SRX9555335.10_summits.bed INFO @ Sat, 11 Dec 2021 10:41:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (83 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 10:41:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555335/SRX9555335.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555335/SRX9555335.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555335/SRX9555335.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555335/SRX9555335.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 10:41:56: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:41:56: #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 10:42:04: #1 tag size is determined as 60 bps INFO @ Sat, 11 Dec 2021 10:42:04: #1 tag size = 60 INFO @ Sat, 11 Dec 2021 10:42:04: #1 total tags in treatment: 281105 INFO @ Sat, 11 Dec 2021 10:42:04: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:42:04: #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 10:42:04: #1 tags after filtering in treatment: 272971 INFO @ Sat, 11 Dec 2021 10:42:04: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 10:42:04: #1 finished! INFO @ Sat, 11 Dec 2021 10:42:04: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:42:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:42:04: #2 number of paired peaks: 1513 INFO @ Sat, 11 Dec 2021 10:42:04: start model_add_line... INFO @ Sat, 11 Dec 2021 10:42:04: start X-correlation... INFO @ Sat, 11 Dec 2021 10:42:04: end of X-cor INFO @ Sat, 11 Dec 2021 10:42:04: #2 finished! INFO @ Sat, 11 Dec 2021 10:42:04: #2 predicted fragment length is 47 bps INFO @ Sat, 11 Dec 2021 10:42:04: #2 alternative fragment length(s) may be 47,492,562 bps INFO @ Sat, 11 Dec 2021 10:42:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555335/SRX9555335.20_model.r WARNING @ Sat, 11 Dec 2021 10:42:04: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 10:42:04: #2 You may need to consider one of the other alternative d(s): 47,492,562 WARNING @ Sat, 11 Dec 2021 10:42:04: #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 10:42:04: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:42:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:42:05: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:42:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555335/SRX9555335.20_peaks.xls INFO @ Sat, 11 Dec 2021 10:42:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555335/SRX9555335.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:42:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555335/SRX9555335.20_summits.bed INFO @ Sat, 11 Dec 2021 10:42:05: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (33 records, 4 fields): 18 millis CompletedMACS2peakCalling