Job ID = 16439274 SRX = SRX15206479 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:48:17 prefetch.2.10.7: 1) Downloading 'SRR19139324'... 2022-08-02T05:48:17 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:48:42 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:48:42 prefetch.2.10.7: 'SRR19139324' is valid 2022-08-02T05:48:42 prefetch.2.10.7: 1) 'SRR19139324' was downloaded successfully 2022-08-02T05:48:42 prefetch.2.10.7: 'SRR19139324' has 0 unresolved dependencies Read 6693431 spots for SRR19139324/SRR19139324.sra Written 6693431 spots for SRR19139324/SRR19139324.sra 2022-08-02T05:49:12 prefetch.2.10.7: 1) Downloading 'SRR19139325'... 2022-08-02T05:49:12 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:49:34 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:49:35 prefetch.2.10.7: 'SRR19139325' is valid 2022-08-02T05:49:35 prefetch.2.10.7: 1) 'SRR19139325' was downloaded successfully 2022-08-02T05:49:35 prefetch.2.10.7: 'SRR19139325' has 0 unresolved dependencies Read 6693431 spots for SRR19139325/SRR19139325.sra Written 6693431 spots for SRR19139325/SRR19139325.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439396 ("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: 00:10:56 13386862 reads; of these: 13386862 (100.00%) were unpaired; of these: 434063 (3.24%) aligned 0 times 7582885 (56.64%) aligned exactly 1 time 5369914 (40.11%) aligned >1 times 96.76% overall alignment rate Time searching: 00:10:56 Overall time: 00:10:56 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 12 files... [bam_rmdupse_core] 6802818 / 12952799 = 0.5252 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 15:06:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206479/SRX15206479.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206479/SRX15206479.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206479/SRX15206479.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206479/SRX15206479.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 15:06:20: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:06:20: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:06:31: 1000000 INFO @ Tue, 02 Aug 2022 15:06:41: 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 15:06:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206479/SRX15206479.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206479/SRX15206479.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206479/SRX15206479.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206479/SRX15206479.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 15:06:49: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:06:49: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:06:52: 3000000 INFO @ Tue, 02 Aug 2022 15:07:01: 1000000 INFO @ Tue, 02 Aug 2022 15:07:03: 4000000 INFO @ Tue, 02 Aug 2022 15:07:13: 2000000 INFO @ Tue, 02 Aug 2022 15:07:15: 5000000 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 15:07:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206479/SRX15206479.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206479/SRX15206479.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206479/SRX15206479.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206479/SRX15206479.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 15:07:19: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:07:19: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:07:24: 3000000 INFO @ Tue, 02 Aug 2022 15:07:27: 6000000 INFO @ Tue, 02 Aug 2022 15:07:28: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 15:07:28: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 15:07:28: #1 total tags in treatment: 6149981 INFO @ Tue, 02 Aug 2022 15:07:28: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:07:28: #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 15:07:28: #1 tags after filtering in treatment: 6149981 INFO @ Tue, 02 Aug 2022 15:07:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:07:28: #1 finished! INFO @ Tue, 02 Aug 2022 15:07:28: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:07:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:07:29: #2 number of paired peaks: 5058 INFO @ Tue, 02 Aug 2022 15:07:29: start model_add_line... INFO @ Tue, 02 Aug 2022 15:07:29: 1000000 INFO @ Tue, 02 Aug 2022 15:07:29: start X-correlation... INFO @ Tue, 02 Aug 2022 15:07:29: end of X-cor INFO @ Tue, 02 Aug 2022 15:07:29: #2 finished! INFO @ Tue, 02 Aug 2022 15:07:29: #2 predicted fragment length is 205 bps INFO @ Tue, 02 Aug 2022 15:07:29: #2 alternative fragment length(s) may be 205 bps INFO @ Tue, 02 Aug 2022 15:07:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206479/SRX15206479.05_model.r WARNING @ Tue, 02 Aug 2022 15:07:29: #2 Since the d (205) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:07:29: #2 You may need to consider one of the other alternative d(s): 205 WARNING @ Tue, 02 Aug 2022 15:07:29: #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 15:07:29: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:07:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:07:36: 4000000 INFO @ Tue, 02 Aug 2022 15:07:39: 2000000 INFO @ Tue, 02 Aug 2022 15:07:47: 5000000 INFO @ Tue, 02 Aug 2022 15:07:48: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:07:49: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:07:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206479/SRX15206479.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:07:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206479/SRX15206479.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:07:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206479/SRX15206479.05_summits.bed INFO @ Tue, 02 Aug 2022 15:07:55: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7378 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:07:58: 6000000 INFO @ Tue, 02 Aug 2022 15:07:59: 4000000 INFO @ Tue, 02 Aug 2022 15:08:00: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 15:08:00: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 15:08:00: #1 total tags in treatment: 6149981 INFO @ Tue, 02 Aug 2022 15:08:00: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:08:00: #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 15:08:00: #1 tags after filtering in treatment: 6149981 INFO @ Tue, 02 Aug 2022 15:08:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:08:00: #1 finished! INFO @ Tue, 02 Aug 2022 15:08:00: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:08:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:08:01: #2 number of paired peaks: 5058 INFO @ Tue, 02 Aug 2022 15:08:01: start model_add_line... INFO @ Tue, 02 Aug 2022 15:08:01: start X-correlation... INFO @ Tue, 02 Aug 2022 15:08:01: end of X-cor INFO @ Tue, 02 Aug 2022 15:08:01: #2 finished! INFO @ Tue, 02 Aug 2022 15:08:01: #2 predicted fragment length is 205 bps INFO @ Tue, 02 Aug 2022 15:08:01: #2 alternative fragment length(s) may be 205 bps INFO @ Tue, 02 Aug 2022 15:08:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206479/SRX15206479.10_model.r WARNING @ Tue, 02 Aug 2022 15:08:01: #2 Since the d (205) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:08:01: #2 You may need to consider one of the other alternative d(s): 205 WARNING @ Tue, 02 Aug 2022 15:08:01: #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 15:08:01: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:08:01: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:08:08: 5000000 INFO @ Tue, 02 Aug 2022 15:08:16: 6000000 INFO @ Tue, 02 Aug 2022 15:08:18: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 15:08:18: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 15:08:18: #1 total tags in treatment: 6149981 INFO @ Tue, 02 Aug 2022 15:08:18: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:08:18: #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 15:08:18: #1 tags after filtering in treatment: 6149981 INFO @ Tue, 02 Aug 2022 15:08:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:08:18: #1 finished! INFO @ Tue, 02 Aug 2022 15:08:18: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:08:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:08:18: #2 number of paired peaks: 5058 INFO @ Tue, 02 Aug 2022 15:08:18: start model_add_line... INFO @ Tue, 02 Aug 2022 15:08:18: start X-correlation... INFO @ Tue, 02 Aug 2022 15:08:18: end of X-cor INFO @ Tue, 02 Aug 2022 15:08:18: #2 finished! INFO @ Tue, 02 Aug 2022 15:08:18: #2 predicted fragment length is 205 bps INFO @ Tue, 02 Aug 2022 15:08:18: #2 alternative fragment length(s) may be 205 bps INFO @ Tue, 02 Aug 2022 15:08:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206479/SRX15206479.20_model.r WARNING @ Tue, 02 Aug 2022 15:08:19: #2 Since the d (205) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:08:19: #2 You may need to consider one of the other alternative d(s): 205 WARNING @ Tue, 02 Aug 2022 15:08:19: #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 15:08:19: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:08:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:08:20: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:08:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206479/SRX15206479.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:08:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206479/SRX15206479.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:08:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206479/SRX15206479.10_summits.bed INFO @ Tue, 02 Aug 2022 15:08:27: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4713 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:08:37: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:08:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206479/SRX15206479.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:08:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206479/SRX15206479.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:08:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206479/SRX15206479.20_summits.bed INFO @ Tue, 02 Aug 2022 15:08:45: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2440 records, 4 fields): 4 millis CompletedMACS2peakCalling