Job ID = 16436189 SRX = SRX15369013 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T02:02:40 prefetch.2.10.7: 1) Downloading 'SRR19308742'... 2022-08-02T02:02:40 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T02:03:14 prefetch.2.10.7: HTTPS download succeed 2022-08-02T02:03:15 prefetch.2.10.7: 'SRR19308742' is valid 2022-08-02T02:03:15 prefetch.2.10.7: 1) 'SRR19308742' was downloaded successfully 2022-08-02T02:03:15 prefetch.2.10.7: 'SRR19308742' has 0 unresolved dependencies Read 17388117 spots for SRR19308742/SRR19308742.sra Written 17388117 spots for SRR19308742/SRR19308742.sra fastq に変換しました。 bowtie でマッピング中... Your job 16436270 ("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: 00:09:22 17388117 reads; of these: 17388117 (100.00%) were unpaired; of these: 807270 (4.64%) aligned 0 times 11443886 (65.81%) aligned exactly 1 time 5136961 (29.54%) aligned >1 times 95.36% overall alignment rate Time searching: 00:09:23 Overall time: 00:09:23 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_sort_core] merging from 8 files... [bam_rmdupse_core] 13072173 / 16580847 = 0.7884 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 11:17:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15369013/SRX15369013.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15369013/SRX15369013.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15369013/SRX15369013.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15369013/SRX15369013.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 11:17:05: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:17:05: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:17:12: 1000000 INFO @ Tue, 02 Aug 2022 11:17:19: 2000000 INFO @ Tue, 02 Aug 2022 11:17:25: 3000000 INFO @ Tue, 02 Aug 2022 11:17:28: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 11:17:28: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 11:17:28: #1 total tags in treatment: 3508674 INFO @ Tue, 02 Aug 2022 11:17:28: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:17:28: #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 11:17:28: #1 tags after filtering in treatment: 3508674 INFO @ Tue, 02 Aug 2022 11:17:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:17:28: #1 finished! INFO @ Tue, 02 Aug 2022 11:17:28: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:17:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:17:29: #2 number of paired peaks: 2551 INFO @ Tue, 02 Aug 2022 11:17:29: start model_add_line... INFO @ Tue, 02 Aug 2022 11:17:29: start X-correlation... INFO @ Tue, 02 Aug 2022 11:17:29: end of X-cor INFO @ Tue, 02 Aug 2022 11:17:29: #2 finished! INFO @ Tue, 02 Aug 2022 11:17:29: #2 predicted fragment length is 81 bps INFO @ Tue, 02 Aug 2022 11:17:29: #2 alternative fragment length(s) may be 81 bps INFO @ Tue, 02 Aug 2022 11:17:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15369013/SRX15369013.05_model.r WARNING @ Tue, 02 Aug 2022 11:17:29: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:17:29: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Tue, 02 Aug 2022 11:17:29: #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 11:17:29: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:17:29: #3 Pre-compute pvalue-qvalue table... 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 11:17:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15369013/SRX15369013.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15369013/SRX15369013.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15369013/SRX15369013.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15369013/SRX15369013.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 11:17:35: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:17:35: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:17:36: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:17:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15369013/SRX15369013.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:17:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15369013/SRX15369013.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:17:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15369013/SRX15369013.05_summits.bed INFO @ Tue, 02 Aug 2022 11:17:41: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5013 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:17:42: 1000000 INFO @ Tue, 02 Aug 2022 11:17:48: 2000000 INFO @ Tue, 02 Aug 2022 11:17:55: 3000000 INFO @ Tue, 02 Aug 2022 11:17:58: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 11:17:58: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 11:17:58: #1 total tags in treatment: 3508674 INFO @ Tue, 02 Aug 2022 11:17:58: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:17:58: #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 11:17:58: #1 tags after filtering in treatment: 3508674 INFO @ Tue, 02 Aug 2022 11:17:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:17:58: #1 finished! INFO @ Tue, 02 Aug 2022 11:17:58: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:17:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:17:58: #2 number of paired peaks: 2551 INFO @ Tue, 02 Aug 2022 11:17:58: start model_add_line... INFO @ Tue, 02 Aug 2022 11:17:58: start X-correlation... INFO @ Tue, 02 Aug 2022 11:17:58: end of X-cor INFO @ Tue, 02 Aug 2022 11:17:58: #2 finished! INFO @ Tue, 02 Aug 2022 11:17:58: #2 predicted fragment length is 81 bps INFO @ Tue, 02 Aug 2022 11:17:58: #2 alternative fragment length(s) may be 81 bps INFO @ Tue, 02 Aug 2022 11:17:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15369013/SRX15369013.10_model.r WARNING @ Tue, 02 Aug 2022 11:17:59: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:17:59: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Tue, 02 Aug 2022 11:17:59: #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 11:17:59: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:17:59: #3 Pre-compute pvalue-qvalue table... 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 11:18:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15369013/SRX15369013.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15369013/SRX15369013.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15369013/SRX15369013.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15369013/SRX15369013.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 11:18:05: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:18:05: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:18:06: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:18:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15369013/SRX15369013.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:18:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15369013/SRX15369013.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:18:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15369013/SRX15369013.10_summits.bed INFO @ Tue, 02 Aug 2022 11:18:10: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1945 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:18:12: 1000000 INFO @ Tue, 02 Aug 2022 11:18:18: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:18:25: 3000000 INFO @ Tue, 02 Aug 2022 11:18:28: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 11:18:28: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 11:18:28: #1 total tags in treatment: 3508674 INFO @ Tue, 02 Aug 2022 11:18:28: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:18:28: #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 11:18:28: #1 tags after filtering in treatment: 3508674 INFO @ Tue, 02 Aug 2022 11:18:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:18:28: #1 finished! INFO @ Tue, 02 Aug 2022 11:18:28: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:18:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:18:28: #2 number of paired peaks: 2551 INFO @ Tue, 02 Aug 2022 11:18:28: start model_add_line... INFO @ Tue, 02 Aug 2022 11:18:28: start X-correlation... INFO @ Tue, 02 Aug 2022 11:18:28: end of X-cor INFO @ Tue, 02 Aug 2022 11:18:28: #2 finished! INFO @ Tue, 02 Aug 2022 11:18:28: #2 predicted fragment length is 81 bps INFO @ Tue, 02 Aug 2022 11:18:28: #2 alternative fragment length(s) may be 81 bps INFO @ Tue, 02 Aug 2022 11:18:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15369013/SRX15369013.20_model.r WARNING @ Tue, 02 Aug 2022 11:18:28: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:18:28: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Tue, 02 Aug 2022 11:18:28: #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 11:18:28: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:18:28: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:18:36: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:18:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15369013/SRX15369013.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:18:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15369013/SRX15369013.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:18:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15369013/SRX15369013.20_summits.bed INFO @ Tue, 02 Aug 2022 11:18:40: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (469 records, 4 fields): 39 millis CompletedMACS2peakCalling