Job ID = 16438946 SRX = SRX15206521 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:13:23 prefetch.2.10.7: 1) Downloading 'SRR19139271'... 2022-08-02T05:13:23 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:14:04 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:14:05 prefetch.2.10.7: 'SRR19139271' is valid 2022-08-02T05:14:05 prefetch.2.10.7: 1) 'SRR19139271' was downloaded successfully 2022-08-02T05:14:05 prefetch.2.10.7: 'SRR19139271' has 0 unresolved dependencies Read 18246254 spots for SRR19139271/SRR19139271.sra Written 18246254 spots for SRR19139271/SRR19139271.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439019 ("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: 00:06:54 18246254 reads; of these: 18246254 (100.00%) were unpaired; of these: 1074065 (5.89%) aligned 0 times 12452980 (68.25%) aligned exactly 1 time 4719209 (25.86%) aligned >1 times 94.11% overall alignment rate Time searching: 00:06:54 Overall time: 00:06:54 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] 8605011 / 17172189 = 0.5011 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 14:25:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206521/SRX15206521.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206521/SRX15206521.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206521/SRX15206521.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206521/SRX15206521.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 14:25:40: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:25:40: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:25:46: 1000000 INFO @ Tue, 02 Aug 2022 14:25:52: 2000000 INFO @ Tue, 02 Aug 2022 14:25:58: 3000000 INFO @ Tue, 02 Aug 2022 14:26:04: 4000000 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 14:26:10: 5000000 INFO @ Tue, 02 Aug 2022 14:26:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206521/SRX15206521.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206521/SRX15206521.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206521/SRX15206521.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206521/SRX15206521.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 14:26:10: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:26:10: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:26:16: 6000000 INFO @ Tue, 02 Aug 2022 14:26:16: 1000000 INFO @ Tue, 02 Aug 2022 14:26:23: 7000000 INFO @ Tue, 02 Aug 2022 14:26:23: 2000000 INFO @ Tue, 02 Aug 2022 14:26:30: 8000000 INFO @ Tue, 02 Aug 2022 14:26:30: 3000000 INFO @ Tue, 02 Aug 2022 14:26:33: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:26:33: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:26:33: #1 total tags in treatment: 8567178 INFO @ Tue, 02 Aug 2022 14:26:33: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:26:33: #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 14:26:33: #1 tags after filtering in treatment: 8567178 INFO @ Tue, 02 Aug 2022 14:26:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:26:33: #1 finished! INFO @ Tue, 02 Aug 2022 14:26:33: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:26:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:26:34: #2 number of paired peaks: 1708 INFO @ Tue, 02 Aug 2022 14:26:34: start model_add_line... INFO @ Tue, 02 Aug 2022 14:26:34: start X-correlation... INFO @ Tue, 02 Aug 2022 14:26:34: end of X-cor INFO @ Tue, 02 Aug 2022 14:26:34: #2 finished! INFO @ Tue, 02 Aug 2022 14:26:34: #2 predicted fragment length is 132 bps INFO @ Tue, 02 Aug 2022 14:26:34: #2 alternative fragment length(s) may be 132 bps INFO @ Tue, 02 Aug 2022 14:26:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206521/SRX15206521.05_model.r WARNING @ Tue, 02 Aug 2022 14:26:34: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:26:34: #2 You may need to consider one of the other alternative d(s): 132 WARNING @ Tue, 02 Aug 2022 14:26:34: #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 14:26:34: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:26:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:26:37: 4000000 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 14:26:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206521/SRX15206521.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206521/SRX15206521.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206521/SRX15206521.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206521/SRX15206521.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 14:26:40: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:26:40: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:26:45: 5000000 INFO @ Tue, 02 Aug 2022 14:26:47: 1000000 INFO @ Tue, 02 Aug 2022 14:26:52: 6000000 INFO @ Tue, 02 Aug 2022 14:26:54: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:26:55: 2000000 INFO @ Tue, 02 Aug 2022 14:26:59: 7000000 INFO @ Tue, 02 Aug 2022 14:27:02: 3000000 INFO @ Tue, 02 Aug 2022 14:27:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206521/SRX15206521.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:27:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206521/SRX15206521.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:27:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206521/SRX15206521.05_summits.bed INFO @ Tue, 02 Aug 2022 14:27:04: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8925 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:27:07: 8000000 INFO @ Tue, 02 Aug 2022 14:27:09: 4000000 INFO @ Tue, 02 Aug 2022 14:27:11: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:27:11: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:27:11: #1 total tags in treatment: 8567178 INFO @ Tue, 02 Aug 2022 14:27:11: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:27:11: #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 14:27:11: #1 tags after filtering in treatment: 8567178 INFO @ Tue, 02 Aug 2022 14:27:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:27:11: #1 finished! INFO @ Tue, 02 Aug 2022 14:27:11: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:27:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:27:12: #2 number of paired peaks: 1708 INFO @ Tue, 02 Aug 2022 14:27:12: start model_add_line... INFO @ Tue, 02 Aug 2022 14:27:12: start X-correlation... INFO @ Tue, 02 Aug 2022 14:27:12: end of X-cor INFO @ Tue, 02 Aug 2022 14:27:12: #2 finished! INFO @ Tue, 02 Aug 2022 14:27:12: #2 predicted fragment length is 132 bps INFO @ Tue, 02 Aug 2022 14:27:12: #2 alternative fragment length(s) may be 132 bps INFO @ Tue, 02 Aug 2022 14:27:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206521/SRX15206521.10_model.r WARNING @ Tue, 02 Aug 2022 14:27:12: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:27:12: #2 You may need to consider one of the other alternative d(s): 132 WARNING @ Tue, 02 Aug 2022 14:27:12: #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 14:27:12: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:27:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:27:16: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:27:22: 6000000 INFO @ Tue, 02 Aug 2022 14:27:28: 7000000 INFO @ Tue, 02 Aug 2022 14:27:31: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:27:34: 8000000 INFO @ Tue, 02 Aug 2022 14:27:37: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:27:37: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:27:37: #1 total tags in treatment: 8567178 INFO @ Tue, 02 Aug 2022 14:27:37: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:27:37: #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 14:27:38: #1 tags after filtering in treatment: 8567178 INFO @ Tue, 02 Aug 2022 14:27:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:27:38: #1 finished! INFO @ Tue, 02 Aug 2022 14:27:38: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:27:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:27:38: #2 number of paired peaks: 1708 INFO @ Tue, 02 Aug 2022 14:27:38: start model_add_line... INFO @ Tue, 02 Aug 2022 14:27:38: start X-correlation... INFO @ Tue, 02 Aug 2022 14:27:38: end of X-cor INFO @ Tue, 02 Aug 2022 14:27:38: #2 finished! INFO @ Tue, 02 Aug 2022 14:27:38: #2 predicted fragment length is 132 bps INFO @ Tue, 02 Aug 2022 14:27:38: #2 alternative fragment length(s) may be 132 bps INFO @ Tue, 02 Aug 2022 14:27:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206521/SRX15206521.20_model.r WARNING @ Tue, 02 Aug 2022 14:27:38: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:27:38: #2 You may need to consider one of the other alternative d(s): 132 WARNING @ Tue, 02 Aug 2022 14:27:38: #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 14:27:38: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:27:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:27:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206521/SRX15206521.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:27:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206521/SRX15206521.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:27:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206521/SRX15206521.10_summits.bed INFO @ Tue, 02 Aug 2022 14:27:41: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (5119 records, 4 fields): 102 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:27:58: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:28:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206521/SRX15206521.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:28:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206521/SRX15206521.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:28:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206521/SRX15206521.20_summits.bed INFO @ Tue, 02 Aug 2022 14:28:08: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2249 records, 4 fields): 78 millis CompletedMACS2peakCalling