Job ID = 14170118 SRX = SRX8556375 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 18179692 spots for SRR12024931/SRR12024931.sra Written 18179692 spots for SRR12024931/SRR12024931.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170693 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:13:31 18179692 reads; of these: 18179692 (100.00%) were paired; of these: 16247336 (89.37%) aligned concordantly 0 times 1470580 (8.09%) aligned concordantly exactly 1 time 461776 (2.54%) aligned concordantly >1 times ---- 16247336 pairs aligned concordantly 0 times; of these: 308604 (1.90%) aligned discordantly 1 time ---- 15938732 pairs aligned 0 times concordantly or discordantly; of these: 31877464 mates make up the pairs; of these: 31073787 (97.48%) aligned 0 times 434281 (1.36%) aligned exactly 1 time 369396 (1.16%) aligned >1 times 14.54% overall alignment rate Time searching: 00:13:32 Overall time: 00:13:32 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] 1593708 / 2208876 = 0.7215 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 05:48:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556375/SRX8556375.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556375/SRX8556375.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556375/SRX8556375.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556375/SRX8556375.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 05:48:46: #1 read tag files... INFO @ Sat, 11 Dec 2021 05:48:46: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 05:48:53: 1000000 INFO @ Sat, 11 Dec 2021 05:49:00: 2000000 INFO @ Sat, 11 Dec 2021 05:49:01: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 05:49:01: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 05:49:01: #1 total tags in treatment: 496159 INFO @ Sat, 11 Dec 2021 05:49:01: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 05:49:01: #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 05:49:01: #1 tags after filtering in treatment: 412330 INFO @ Sat, 11 Dec 2021 05:49:01: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 11 Dec 2021 05:49:01: #1 finished! INFO @ Sat, 11 Dec 2021 05:49:01: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 05:49:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 05:49:01: #2 number of paired peaks: 2940 INFO @ Sat, 11 Dec 2021 05:49:01: start model_add_line... INFO @ Sat, 11 Dec 2021 05:49:01: start X-correlation... INFO @ Sat, 11 Dec 2021 05:49:01: end of X-cor INFO @ Sat, 11 Dec 2021 05:49:01: #2 finished! INFO @ Sat, 11 Dec 2021 05:49:01: #2 predicted fragment length is 170 bps INFO @ Sat, 11 Dec 2021 05:49:01: #2 alternative fragment length(s) may be 170 bps INFO @ Sat, 11 Dec 2021 05:49:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556375/SRX8556375.05_model.r WARNING @ Sat, 11 Dec 2021 05:49:01: #2 Since the d (170) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 05:49:01: #2 You may need to consider one of the other alternative d(s): 170 WARNING @ Sat, 11 Dec 2021 05:49:01: #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 05:49:01: #3 Call peaks... INFO @ Sat, 11 Dec 2021 05:49:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 05:49:02: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 05:49:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556375/SRX8556375.05_peaks.xls INFO @ Sat, 11 Dec 2021 05:49:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556375/SRX8556375.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 05:49:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556375/SRX8556375.05_summits.bed INFO @ Sat, 11 Dec 2021 05:49:03: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1517 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 05:49:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556375/SRX8556375.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556375/SRX8556375.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556375/SRX8556375.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556375/SRX8556375.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 05:49:15: #1 read tag files... INFO @ Sat, 11 Dec 2021 05:49:15: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 05:49:22: 1000000 INFO @ Sat, 11 Dec 2021 05:49:29: 2000000 INFO @ Sat, 11 Dec 2021 05:49:30: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 05:49:30: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 05:49:30: #1 total tags in treatment: 496159 INFO @ Sat, 11 Dec 2021 05:49:30: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 05:49:30: #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 05:49:30: #1 tags after filtering in treatment: 412330 INFO @ Sat, 11 Dec 2021 05:49:30: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 11 Dec 2021 05:49:30: #1 finished! INFO @ Sat, 11 Dec 2021 05:49:30: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 05:49:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 05:49:30: #2 number of paired peaks: 2940 INFO @ Sat, 11 Dec 2021 05:49:30: start model_add_line... INFO @ Sat, 11 Dec 2021 05:49:30: start X-correlation... INFO @ Sat, 11 Dec 2021 05:49:30: end of X-cor INFO @ Sat, 11 Dec 2021 05:49:30: #2 finished! INFO @ Sat, 11 Dec 2021 05:49:30: #2 predicted fragment length is 170 bps INFO @ Sat, 11 Dec 2021 05:49:30: #2 alternative fragment length(s) may be 170 bps INFO @ Sat, 11 Dec 2021 05:49:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556375/SRX8556375.10_model.r WARNING @ Sat, 11 Dec 2021 05:49:30: #2 Since the d (170) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 05:49:30: #2 You may need to consider one of the other alternative d(s): 170 WARNING @ Sat, 11 Dec 2021 05:49:30: #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 05:49:30: #3 Call peaks... INFO @ Sat, 11 Dec 2021 05:49:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 05:49:31: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 05:49:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556375/SRX8556375.10_peaks.xls INFO @ Sat, 11 Dec 2021 05:49:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556375/SRX8556375.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 05:49:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556375/SRX8556375.10_summits.bed INFO @ Sat, 11 Dec 2021 05:49:32: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (918 records, 4 fields): 9 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 05:49:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8556375/SRX8556375.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8556375/SRX8556375.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8556375/SRX8556375.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8556375/SRX8556375.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 05:49:45: #1 read tag files... INFO @ Sat, 11 Dec 2021 05:49:45: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 05:49:52: 1000000 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 05:50:00: 2000000 INFO @ Sat, 11 Dec 2021 05:50:00: #1 tag size is determined as 150 bps INFO @ Sat, 11 Dec 2021 05:50:00: #1 tag size = 150 INFO @ Sat, 11 Dec 2021 05:50:00: #1 total tags in treatment: 496159 INFO @ Sat, 11 Dec 2021 05:50:00: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 05:50:00: #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 05:50:00: #1 tags after filtering in treatment: 412330 INFO @ Sat, 11 Dec 2021 05:50:00: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 11 Dec 2021 05:50:00: #1 finished! INFO @ Sat, 11 Dec 2021 05:50:00: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 05:50:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 05:50:01: #2 number of paired peaks: 2940 INFO @ Sat, 11 Dec 2021 05:50:01: start model_add_line... INFO @ Sat, 11 Dec 2021 05:50:01: start X-correlation... INFO @ Sat, 11 Dec 2021 05:50:01: end of X-cor INFO @ Sat, 11 Dec 2021 05:50:01: #2 finished! INFO @ Sat, 11 Dec 2021 05:50:01: #2 predicted fragment length is 170 bps INFO @ Sat, 11 Dec 2021 05:50:01: #2 alternative fragment length(s) may be 170 bps INFO @ Sat, 11 Dec 2021 05:50:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8556375/SRX8556375.20_model.r WARNING @ Sat, 11 Dec 2021 05:50:01: #2 Since the d (170) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 05:50:01: #2 You may need to consider one of the other alternative d(s): 170 WARNING @ Sat, 11 Dec 2021 05:50:01: #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 05:50:01: #3 Call peaks... INFO @ Sat, 11 Dec 2021 05:50:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 05:50:02: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 05:50:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8556375/SRX8556375.20_peaks.xls INFO @ Sat, 11 Dec 2021 05:50:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8556375/SRX8556375.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 05:50:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8556375/SRX8556375.20_summits.bed INFO @ Sat, 11 Dec 2021 05:50:02: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (476 records, 4 fields): 1 millis CompletedMACS2peakCalling