Job ID = 16438133 SRX = SRX12839276 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-08-02T04:42:02 prefetch.2.10.7: 1) Downloading 'SRR16638477'... 2022-08-02T04:42:02 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T04:42:18 prefetch.2.10.7: HTTPS download succeed 2022-08-02T04:42:19 prefetch.2.10.7: 'SRR16638477' is valid 2022-08-02T04:42:19 prefetch.2.10.7: 1) 'SRR16638477' was downloaded successfully 2022-08-02T04:42:19 prefetch.2.10.7: 'SRR16638477' has 0 unresolved dependencies Read 1790952 spots for SRR16638477/SRR16638477.sra Written 1790952 spots for SRR16638477/SRR16638477.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438505 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:14 1790952 reads; of these: 1790952 (100.00%) were paired; of these: 284835 (15.90%) aligned concordantly 0 times 1086964 (60.69%) aligned concordantly exactly 1 time 419153 (23.40%) aligned concordantly >1 times ---- 284835 pairs aligned concordantly 0 times; of these: 70339 (24.69%) aligned discordantly 1 time ---- 214496 pairs aligned 0 times concordantly or discordantly; of these: 428992 mates make up the pairs; of these: 307353 (71.65%) aligned 0 times 41500 (9.67%) aligned exactly 1 time 80139 (18.68%) aligned >1 times 91.42% overall alignment rate Time searching: 00:06:15 Overall time: 00:06:15 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] 139894 / 1569894 = 0.0891 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:50:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12839276/SRX12839276.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12839276/SRX12839276.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12839276/SRX12839276.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12839276/SRX12839276.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 @ Tue, 02 Aug 2022 13:50:48: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:50:48: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:50:59: 1000000 INFO @ Tue, 02 Aug 2022 13:51:10: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:51:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12839276/SRX12839276.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12839276/SRX12839276.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12839276/SRX12839276.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12839276/SRX12839276.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 @ Tue, 02 Aug 2022 13:51:17: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:51:17: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:51:22: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 13:51:22: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 13:51:22: #1 total tags in treatment: 1369792 INFO @ Tue, 02 Aug 2022 13:51:22: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:51:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 13:51:22: #1 tags after filtering in treatment: 1340800 INFO @ Tue, 02 Aug 2022 13:51:22: #1 Redundant rate of treatment: 0.02 INFO @ Tue, 02 Aug 2022 13:51:22: #1 finished! INFO @ Tue, 02 Aug 2022 13:51:22: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:51:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:51:22: #2 number of paired peaks: 1232 INFO @ Tue, 02 Aug 2022 13:51:22: start model_add_line... INFO @ Tue, 02 Aug 2022 13:51:22: start X-correlation... INFO @ Tue, 02 Aug 2022 13:51:22: end of X-cor INFO @ Tue, 02 Aug 2022 13:51:22: #2 finished! INFO @ Tue, 02 Aug 2022 13:51:22: #2 predicted fragment length is 213 bps INFO @ Tue, 02 Aug 2022 13:51:22: #2 alternative fragment length(s) may be 213 bps INFO @ Tue, 02 Aug 2022 13:51:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12839276/SRX12839276.05_model.r WARNING @ Tue, 02 Aug 2022 13:51:22: #2 Since the d (213) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:51:22: #2 You may need to consider one of the other alternative d(s): 213 WARNING @ Tue, 02 Aug 2022 13:51:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 13:51:22: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:51:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:51:25: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:51:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12839276/SRX12839276.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:51:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12839276/SRX12839276.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:51:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12839276/SRX12839276.05_summits.bed INFO @ Tue, 02 Aug 2022 13:51:27: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (647 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:51:28: 1000000 INFO @ Tue, 02 Aug 2022 13:51:38: 2000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:51:47: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 13:51:47: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 13:51:47: #1 total tags in treatment: 1369792 INFO @ Tue, 02 Aug 2022 13:51:47: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:51:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 13:51:47: #1 tags after filtering in treatment: 1340800 INFO @ Tue, 02 Aug 2022 13:51:47: #1 Redundant rate of treatment: 0.02 INFO @ Tue, 02 Aug 2022 13:51:47: #1 finished! INFO @ Tue, 02 Aug 2022 13:51:47: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:51:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:51:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12839276/SRX12839276.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12839276/SRX12839276.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12839276/SRX12839276.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12839276/SRX12839276.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 @ Tue, 02 Aug 2022 13:51:47: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:51:47: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:51:47: #2 number of paired peaks: 1232 INFO @ Tue, 02 Aug 2022 13:51:47: start model_add_line... INFO @ Tue, 02 Aug 2022 13:51:47: start X-correlation... INFO @ Tue, 02 Aug 2022 13:51:47: end of X-cor INFO @ Tue, 02 Aug 2022 13:51:47: #2 finished! INFO @ Tue, 02 Aug 2022 13:51:47: #2 predicted fragment length is 213 bps INFO @ Tue, 02 Aug 2022 13:51:47: #2 alternative fragment length(s) may be 213 bps INFO @ Tue, 02 Aug 2022 13:51:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12839276/SRX12839276.10_model.r WARNING @ Tue, 02 Aug 2022 13:51:47: #2 Since the d (213) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:51:47: #2 You may need to consider one of the other alternative d(s): 213 WARNING @ Tue, 02 Aug 2022 13:51:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 13:51:47: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:51:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:51:51: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:51:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12839276/SRX12839276.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:51:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12839276/SRX12839276.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:51:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12839276/SRX12839276.10_summits.bed INFO @ Tue, 02 Aug 2022 13:51:52: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (379 records, 4 fields): 41 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:51:57: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:52:07: 2000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 13:52:17: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 13:52:17: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 13:52:17: #1 total tags in treatment: 1369792 INFO @ Tue, 02 Aug 2022 13:52:17: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:52:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 13:52:17: #1 tags after filtering in treatment: 1340800 INFO @ Tue, 02 Aug 2022 13:52:17: #1 Redundant rate of treatment: 0.02 INFO @ Tue, 02 Aug 2022 13:52:17: #1 finished! INFO @ Tue, 02 Aug 2022 13:52:17: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:52:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:52:17: #2 number of paired peaks: 1232 INFO @ Tue, 02 Aug 2022 13:52:17: start model_add_line... INFO @ Tue, 02 Aug 2022 13:52:17: start X-correlation... INFO @ Tue, 02 Aug 2022 13:52:17: end of X-cor INFO @ Tue, 02 Aug 2022 13:52:17: #2 finished! INFO @ Tue, 02 Aug 2022 13:52:17: #2 predicted fragment length is 213 bps INFO @ Tue, 02 Aug 2022 13:52:17: #2 alternative fragment length(s) may be 213 bps INFO @ Tue, 02 Aug 2022 13:52:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12839276/SRX12839276.20_model.r WARNING @ Tue, 02 Aug 2022 13:52:17: #2 Since the d (213) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:52:17: #2 You may need to consider one of the other alternative d(s): 213 WARNING @ Tue, 02 Aug 2022 13:52:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 13:52:17: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:52:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:52:20: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:52:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12839276/SRX12839276.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:52:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12839276/SRX12839276.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:52:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12839276/SRX12839276.20_summits.bed INFO @ Tue, 02 Aug 2022 13:52:22: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (171 records, 4 fields): 34 millis CompletedMACS2peakCalling