Job ID = 16438131 SRX = SRX12839274 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-08-02T04:40:57 prefetch.2.10.7: 1) Downloading 'SRR16638475'... 2022-08-02T04:40:57 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T04:41:51 prefetch.2.10.7: HTTPS download succeed 2022-08-02T04:41:51 prefetch.2.10.7: 'SRR16638475' is valid 2022-08-02T04:41:51 prefetch.2.10.7: 1) 'SRR16638475' was downloaded successfully 2022-08-02T04:41:51 prefetch.2.10.7: 'SRR16638475' has 0 unresolved dependencies Read 2880763 spots for SRR16638475/SRR16638475.sra Written 2880763 spots for SRR16638475/SRR16638475.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438508 ("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: 00:07:22 2880763 reads; of these: 2880763 (100.00%) were paired; of these: 1055499 (36.64%) aligned concordantly 0 times 1447887 (50.26%) aligned concordantly exactly 1 time 377377 (13.10%) aligned concordantly >1 times ---- 1055499 pairs aligned concordantly 0 times; of these: 182146 (17.26%) aligned discordantly 1 time ---- 873353 pairs aligned 0 times concordantly or discordantly; of these: 1746706 mates make up the pairs; of these: 1523810 (87.24%) aligned 0 times 83124 (4.76%) aligned exactly 1 time 139772 (8.00%) aligned >1 times 73.55% overall alignment rate Time searching: 00:07:22 Overall time: 00:07:22 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] 231805 / 2001525 = 0.1158 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 13:52:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12839274/SRX12839274.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12839274/SRX12839274.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12839274/SRX12839274.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12839274/SRX12839274.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 13:52:03: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:52:03: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:52:12: 1000000 INFO @ Tue, 02 Aug 2022 13:52:20: 2000000 INFO @ Tue, 02 Aug 2022 13:52:28: 3000000 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 13:52:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12839274/SRX12839274.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12839274/SRX12839274.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12839274/SRX12839274.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12839274/SRX12839274.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 13:52:33: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:52:33: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:52:35: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 13:52:35: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 13:52:35: #1 total tags in treatment: 1606752 INFO @ Tue, 02 Aug 2022 13:52:35: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:52:35: #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 13:52:35: #1 tags after filtering in treatment: 1551087 INFO @ Tue, 02 Aug 2022 13:52:35: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 13:52:35: #1 finished! INFO @ Tue, 02 Aug 2022 13:52:35: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:52:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:52:35: #2 number of paired peaks: 4293 INFO @ Tue, 02 Aug 2022 13:52:35: start model_add_line... INFO @ Tue, 02 Aug 2022 13:52:35: start X-correlation... INFO @ Tue, 02 Aug 2022 13:52:35: end of X-cor INFO @ Tue, 02 Aug 2022 13:52:35: #2 finished! INFO @ Tue, 02 Aug 2022 13:52:35: #2 predicted fragment length is 259 bps INFO @ Tue, 02 Aug 2022 13:52:35: #2 alternative fragment length(s) may be 259 bps INFO @ Tue, 02 Aug 2022 13:52:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12839274/SRX12839274.05_model.r WARNING @ Tue, 02 Aug 2022 13:52:36: #2 Since the d (259) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:52:36: #2 You may need to consider one of the other alternative d(s): 259 WARNING @ Tue, 02 Aug 2022 13:52:36: #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 13:52:36: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:52:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:52:39: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:52:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12839274/SRX12839274.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:52:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12839274/SRX12839274.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:52:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12839274/SRX12839274.05_summits.bed INFO @ Tue, 02 Aug 2022 13:52:42: Done! INFO @ Tue, 02 Aug 2022 13:52:42: 1000000 pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3630 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:52:50: 2000000 INFO @ Tue, 02 Aug 2022 13:52:58: 3000000 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 13:53:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12839274/SRX12839274.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12839274/SRX12839274.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12839274/SRX12839274.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12839274/SRX12839274.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 13:53:03: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:53:03: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:53:05: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 13:53:05: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 13:53:05: #1 total tags in treatment: 1606752 INFO @ Tue, 02 Aug 2022 13:53:05: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:53:05: #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 13:53:05: #1 tags after filtering in treatment: 1551087 INFO @ Tue, 02 Aug 2022 13:53:05: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 13:53:05: #1 finished! INFO @ Tue, 02 Aug 2022 13:53:05: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:53:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:53:05: #2 number of paired peaks: 4293 INFO @ Tue, 02 Aug 2022 13:53:05: start model_add_line... INFO @ Tue, 02 Aug 2022 13:53:05: start X-correlation... INFO @ Tue, 02 Aug 2022 13:53:05: end of X-cor INFO @ Tue, 02 Aug 2022 13:53:05: #2 finished! INFO @ Tue, 02 Aug 2022 13:53:05: #2 predicted fragment length is 259 bps INFO @ Tue, 02 Aug 2022 13:53:05: #2 alternative fragment length(s) may be 259 bps INFO @ Tue, 02 Aug 2022 13:53:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12839274/SRX12839274.10_model.r WARNING @ Tue, 02 Aug 2022 13:53:06: #2 Since the d (259) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:53:06: #2 You may need to consider one of the other alternative d(s): 259 WARNING @ Tue, 02 Aug 2022 13:53:06: #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 13:53:06: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:53:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:53:10: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:53:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12839274/SRX12839274.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:53:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12839274/SRX12839274.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:53:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12839274/SRX12839274.10_summits.bed INFO @ Tue, 02 Aug 2022 13:53:12: Done! INFO @ Tue, 02 Aug 2022 13:53:12: 1000000 pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (2316 records, 4 fields): 58 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:53:21: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:53:29: 3000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 13:53:35: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 13:53:35: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 13:53:35: #1 total tags in treatment: 1606752 INFO @ Tue, 02 Aug 2022 13:53:35: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:53:35: #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 13:53:35: #1 tags after filtering in treatment: 1551087 INFO @ Tue, 02 Aug 2022 13:53:35: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 13:53:35: #1 finished! INFO @ Tue, 02 Aug 2022 13:53:35: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:53:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:53:36: #2 number of paired peaks: 4293 INFO @ Tue, 02 Aug 2022 13:53:36: start model_add_line... INFO @ Tue, 02 Aug 2022 13:53:36: start X-correlation... INFO @ Tue, 02 Aug 2022 13:53:36: end of X-cor INFO @ Tue, 02 Aug 2022 13:53:36: #2 finished! INFO @ Tue, 02 Aug 2022 13:53:36: #2 predicted fragment length is 259 bps INFO @ Tue, 02 Aug 2022 13:53:36: #2 alternative fragment length(s) may be 259 bps INFO @ Tue, 02 Aug 2022 13:53:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12839274/SRX12839274.20_model.r WARNING @ Tue, 02 Aug 2022 13:53:36: #2 Since the d (259) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:53:36: #2 You may need to consider one of the other alternative d(s): 259 WARNING @ Tue, 02 Aug 2022 13:53:36: #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 13:53:36: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:53:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:53:40: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:53:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12839274/SRX12839274.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:53:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12839274/SRX12839274.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:53:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12839274/SRX12839274.20_summits.bed INFO @ Tue, 02 Aug 2022 13:53:42: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1307 records, 4 fields): 26 millis CompletedMACS2peakCalling