Job ID = 14171444 SRX = SRX9555291 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12539156 spots for SRR13110735/SRR13110735.sra Written 12539156 spots for SRR13110735/SRR13110735.sra Read 12409517 spots for SRR13110736/SRR13110736.sra Written 12409517 spots for SRR13110736/SRR13110736.sra Read 12598814 spots for SRR13110737/SRR13110737.sra Written 12598814 spots for SRR13110737/SRR13110737.sra Read 12472001 spots for SRR13110738/SRR13110738.sra Written 12472001 spots for SRR13110738/SRR13110738.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171966 ("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: 00:08:02 50019488 reads; of these: 50019488 (100.00%) were paired; of these: 47881815 (95.73%) aligned concordantly 0 times 1674288 (3.35%) aligned concordantly exactly 1 time 463385 (0.93%) aligned concordantly >1 times ---- 47881815 pairs aligned concordantly 0 times; of these: 3951 (0.01%) aligned discordantly 1 time ---- 47877864 pairs aligned 0 times concordantly or discordantly; of these: 95755728 mates make up the pairs; of these: 95430768 (99.66%) aligned 0 times 123528 (0.13%) aligned exactly 1 time 201432 (0.21%) aligned >1 times 4.61% overall alignment rate Time searching: 00:08:02 Overall time: 00:08:02 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] 139985 / 2140510 = 0.0654 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 11:54:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555291/SRX9555291.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555291/SRX9555291.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555291/SRX9555291.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555291/SRX9555291.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 11:54:07: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:54:07: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:54:13: 1000000 INFO @ Sat, 11 Dec 2021 11:54:18: 2000000 INFO @ Sat, 11 Dec 2021 11:54:23: 3000000 INFO @ Sat, 11 Dec 2021 11:54:28: 4000000 INFO @ Sat, 11 Dec 2021 11:54:29: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:54:29: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:54:29: #1 total tags in treatment: 1997757 INFO @ Sat, 11 Dec 2021 11:54:29: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:54:29: #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 11:54:30: #1 tags after filtering in treatment: 1687658 INFO @ Sat, 11 Dec 2021 11:54:30: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 11 Dec 2021 11:54:30: #1 finished! INFO @ Sat, 11 Dec 2021 11:54:30: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:54:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:54:30: #2 number of paired peaks: 8047 INFO @ Sat, 11 Dec 2021 11:54:30: start model_add_line... INFO @ Sat, 11 Dec 2021 11:54:30: start X-correlation... INFO @ Sat, 11 Dec 2021 11:54:30: end of X-cor INFO @ Sat, 11 Dec 2021 11:54:30: #2 finished! INFO @ Sat, 11 Dec 2021 11:54:30: #2 predicted fragment length is 155 bps INFO @ Sat, 11 Dec 2021 11:54:30: #2 alternative fragment length(s) may be 155 bps INFO @ Sat, 11 Dec 2021 11:54:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555291/SRX9555291.05_model.r INFO @ Sat, 11 Dec 2021 11:54:30: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:54:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:54:34: #3 Call peaks for each chromosome... 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 11:54:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555291/SRX9555291.05_peaks.xls INFO @ Sat, 11 Dec 2021 11:54:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555291/SRX9555291.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:54:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555291/SRX9555291.05_summits.bed INFO @ Sat, 11 Dec 2021 11:54:36: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4923 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 11:54:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555291/SRX9555291.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555291/SRX9555291.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555291/SRX9555291.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555291/SRX9555291.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 11:54:37: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:54:37: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:54:42: 1000000 INFO @ Sat, 11 Dec 2021 11:54:47: 2000000 INFO @ Sat, 11 Dec 2021 11:54:52: 3000000 INFO @ Sat, 11 Dec 2021 11:54:56: 4000000 INFO @ Sat, 11 Dec 2021 11:54:58: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:54:58: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:54:58: #1 total tags in treatment: 1997757 INFO @ Sat, 11 Dec 2021 11:54:58: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:54:58: #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 11:54:58: #1 tags after filtering in treatment: 1687658 INFO @ Sat, 11 Dec 2021 11:54:58: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 11 Dec 2021 11:54:58: #1 finished! INFO @ Sat, 11 Dec 2021 11:54:58: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:54:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:54:58: #2 number of paired peaks: 8047 INFO @ Sat, 11 Dec 2021 11:54:58: start model_add_line... INFO @ Sat, 11 Dec 2021 11:54:58: start X-correlation... INFO @ Sat, 11 Dec 2021 11:54:58: end of X-cor INFO @ Sat, 11 Dec 2021 11:54:58: #2 finished! INFO @ Sat, 11 Dec 2021 11:54:58: #2 predicted fragment length is 155 bps INFO @ Sat, 11 Dec 2021 11:54:58: #2 alternative fragment length(s) may be 155 bps INFO @ Sat, 11 Dec 2021 11:54:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555291/SRX9555291.10_model.r INFO @ Sat, 11 Dec 2021 11:54:58: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:54:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 11:55:02: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:55:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555291/SRX9555291.10_peaks.xls INFO @ Sat, 11 Dec 2021 11:55:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555291/SRX9555291.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:55:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555291/SRX9555291.10_summits.bed INFO @ Sat, 11 Dec 2021 11:55:04: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1927 records, 4 fields): 4 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 11:55:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9555291/SRX9555291.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9555291/SRX9555291.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9555291/SRX9555291.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9555291/SRX9555291.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 11:55:07: #1 read tag files... INFO @ Sat, 11 Dec 2021 11:55:07: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 11:55:12: 1000000 INFO @ Sat, 11 Dec 2021 11:55:17: 2000000 INFO @ Sat, 11 Dec 2021 11:55:22: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 11:55:27: 4000000 INFO @ Sat, 11 Dec 2021 11:55:28: #1 tag size is determined as 39 bps INFO @ Sat, 11 Dec 2021 11:55:28: #1 tag size = 39 INFO @ Sat, 11 Dec 2021 11:55:28: #1 total tags in treatment: 1997757 INFO @ Sat, 11 Dec 2021 11:55:28: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 11:55:28: #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 11:55:28: #1 tags after filtering in treatment: 1687658 INFO @ Sat, 11 Dec 2021 11:55:28: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 11 Dec 2021 11:55:28: #1 finished! INFO @ Sat, 11 Dec 2021 11:55:28: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 11:55:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 11:55:29: #2 number of paired peaks: 8047 INFO @ Sat, 11 Dec 2021 11:55:29: start model_add_line... INFO @ Sat, 11 Dec 2021 11:55:29: start X-correlation... INFO @ Sat, 11 Dec 2021 11:55:29: end of X-cor INFO @ Sat, 11 Dec 2021 11:55:29: #2 finished! INFO @ Sat, 11 Dec 2021 11:55:29: #2 predicted fragment length is 155 bps INFO @ Sat, 11 Dec 2021 11:55:29: #2 alternative fragment length(s) may be 155 bps INFO @ Sat, 11 Dec 2021 11:55:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9555291/SRX9555291.20_model.r INFO @ Sat, 11 Dec 2021 11:55:29: #3 Call peaks... INFO @ Sat, 11 Dec 2021 11:55:29: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 11:55:33: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 11:55:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9555291/SRX9555291.20_peaks.xls INFO @ Sat, 11 Dec 2021 11:55:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9555291/SRX9555291.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 11:55:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9555291/SRX9555291.20_summits.bed INFO @ Sat, 11 Dec 2021 11:55:35: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (483 records, 4 fields): 1 millis CompletedMACS2peakCalling