Job ID = 14171201 SRX = SRX9555330 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5974585 spots for SRR13110825/SRR13110825.sra Written 5974585 spots for SRR13110825/SRR13110825.sra Read 5814708 spots for SRR13110826/SRR13110826.sra Written 5814708 spots for SRR13110826/SRR13110826.sra Read 5979230 spots for SRR13110827/SRR13110827.sra Written 5979230 spots for SRR13110827/SRR13110827.sra Read 5881144 spots for SRR13110828/SRR13110828.sra Written 5881144 spots for SRR13110828/SRR13110828.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171690 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:05:58 23649667 reads; of these: 23649667 (100.00%) were paired; of these: 23198525 (98.09%) aligned concordantly 0 times 325460 (1.38%) aligned concordantly exactly 1 time 125682 (0.53%) aligned concordantly >1 times ---- 23198525 pairs aligned concordantly 0 times; of these: 7344 (0.03%) aligned discordantly 1 time ---- 23191181 pairs aligned 0 times concordantly or discordantly; of these: 46382362 mates make up the pairs; of these: 46323004 (99.87%) aligned 0 times 14548 (0.03%) aligned exactly 1 time 44810 (0.10%) aligned >1 times 2.06% overall alignment rate Time searching: 00:05:59 Overall time: 00:05:59 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] 7279 / 339955 = 0.0214 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 10:42:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555330/SRX9555330.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555330/SRX9555330.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555330/SRX9555330.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555330/SRX9555330.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 10:42:54: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:42:54: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:43:02: #1 tag size is determined as 79 bps INFO @ Sat, 11 Dec 2021 10:43:02: #1 tag size = 79 INFO @ Sat, 11 Dec 2021 10:43:02: #1 total tags in treatment: 443925 INFO @ Sat, 11 Dec 2021 10:43:02: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:43:02: #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 10:43:02: #1 tags after filtering in treatment: 423824 INFO @ Sat, 11 Dec 2021 10:43:02: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 11 Dec 2021 10:43:02: #1 finished! INFO @ Sat, 11 Dec 2021 10:43:02: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:43:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:43:02: #2 number of paired peaks: 4133 INFO @ Sat, 11 Dec 2021 10:43:02: start model_add_line... INFO @ Sat, 11 Dec 2021 10:43:02: start X-correlation... INFO @ Sat, 11 Dec 2021 10:43:02: end of X-cor INFO @ Sat, 11 Dec 2021 10:43:02: #2 finished! INFO @ Sat, 11 Dec 2021 10:43:02: #2 predicted fragment length is 123 bps INFO @ Sat, 11 Dec 2021 10:43:02: #2 alternative fragment length(s) may be 123 bps INFO @ Sat, 11 Dec 2021 10:43:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555330/SRX9555330.05_model.r WARNING @ Sat, 11 Dec 2021 10:43:02: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 10:43:02: #2 You may need to consider one of the other alternative d(s): 123 WARNING @ Sat, 11 Dec 2021 10:43:02: #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 10:43:02: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:43:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:43:03: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:43:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555330/SRX9555330.05_peaks.xls INFO @ Sat, 11 Dec 2021 10:43:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555330/SRX9555330.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:43:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555330/SRX9555330.05_summits.bed INFO @ Sat, 11 Dec 2021 10:43:04: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (465 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 10:43:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555330/SRX9555330.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555330/SRX9555330.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555330/SRX9555330.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555330/SRX9555330.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 10:43:25: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:43:25: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 10:43:32: #1 tag size is determined as 79 bps INFO @ Sat, 11 Dec 2021 10:43:32: #1 tag size = 79 INFO @ Sat, 11 Dec 2021 10:43:32: #1 total tags in treatment: 443925 INFO @ Sat, 11 Dec 2021 10:43:32: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:43:32: #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 10:43:32: #1 tags after filtering in treatment: 423824 INFO @ Sat, 11 Dec 2021 10:43:32: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 11 Dec 2021 10:43:32: #1 finished! INFO @ Sat, 11 Dec 2021 10:43:32: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:43:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:43:32: #2 number of paired peaks: 4133 INFO @ Sat, 11 Dec 2021 10:43:32: start model_add_line... INFO @ Sat, 11 Dec 2021 10:43:32: start X-correlation... INFO @ Sat, 11 Dec 2021 10:43:32: end of X-cor INFO @ Sat, 11 Dec 2021 10:43:32: #2 finished! INFO @ Sat, 11 Dec 2021 10:43:32: #2 predicted fragment length is 123 bps INFO @ Sat, 11 Dec 2021 10:43:32: #2 alternative fragment length(s) may be 123 bps INFO @ Sat, 11 Dec 2021 10:43:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555330/SRX9555330.10_model.r WARNING @ Sat, 11 Dec 2021 10:43:32: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 10:43:32: #2 You may need to consider one of the other alternative d(s): 123 WARNING @ Sat, 11 Dec 2021 10:43:32: #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 10:43:32: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:43:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:43:33: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:43:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555330/SRX9555330.10_peaks.xls INFO @ Sat, 11 Dec 2021 10:43:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555330/SRX9555330.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:43:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555330/SRX9555330.10_summits.bed INFO @ Sat, 11 Dec 2021 10:43:34: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (171 records, 4 fields): 3 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 10:43:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555330/SRX9555330.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555330/SRX9555330.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555330/SRX9555330.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555330/SRX9555330.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 10:43:55: #1 read tag files... INFO @ Sat, 11 Dec 2021 10:43:55: #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 10:44:02: #1 tag size is determined as 79 bps INFO @ Sat, 11 Dec 2021 10:44:02: #1 tag size = 79 INFO @ Sat, 11 Dec 2021 10:44:02: #1 total tags in treatment: 443925 INFO @ Sat, 11 Dec 2021 10:44:02: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 10:44:02: #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 10:44:02: #1 tags after filtering in treatment: 423824 INFO @ Sat, 11 Dec 2021 10:44:02: #1 Redundant rate of treatment: 0.05 INFO @ Sat, 11 Dec 2021 10:44:02: #1 finished! INFO @ Sat, 11 Dec 2021 10:44:02: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 10:44:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 10:44:02: #2 number of paired peaks: 4133 INFO @ Sat, 11 Dec 2021 10:44:02: start model_add_line... INFO @ Sat, 11 Dec 2021 10:44:02: start X-correlation... INFO @ Sat, 11 Dec 2021 10:44:02: end of X-cor INFO @ Sat, 11 Dec 2021 10:44:02: #2 finished! INFO @ Sat, 11 Dec 2021 10:44:02: #2 predicted fragment length is 123 bps INFO @ Sat, 11 Dec 2021 10:44:02: #2 alternative fragment length(s) may be 123 bps INFO @ Sat, 11 Dec 2021 10:44:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555330/SRX9555330.20_model.r WARNING @ Sat, 11 Dec 2021 10:44:02: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 10:44:02: #2 You may need to consider one of the other alternative d(s): 123 WARNING @ Sat, 11 Dec 2021 10:44:02: #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 10:44:02: #3 Call peaks... INFO @ Sat, 11 Dec 2021 10:44:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 10:44:03: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 10:44:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555330/SRX9555330.20_peaks.xls INFO @ Sat, 11 Dec 2021 10:44:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555330/SRX9555330.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 10:44:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555330/SRX9555330.20_summits.bed INFO @ Sat, 11 Dec 2021 10:44:04: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (71 records, 4 fields): 2 millis CompletedMACS2peakCalling