Job ID = 16438692 SRX = SRX15206505 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:04:56 prefetch.2.10.7: 1) Downloading 'SRR19139287'... 2022-08-02T05:04:56 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:05:26 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:05:27 prefetch.2.10.7: 'SRR19139287' is valid 2022-08-02T05:05:27 prefetch.2.10.7: 1) 'SRR19139287' was downloaded successfully 2022-08-02T05:05:27 prefetch.2.10.7: 'SRR19139287' has 0 unresolved dependencies Read 19393659 spots for SRR19139287/SRR19139287.sra Written 19393659 spots for SRR19139287/SRR19139287.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439001 ("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: 00:12:43 19393659 reads; of these: 19393659 (100.00%) were unpaired; of these: 196980 (1.02%) aligned 0 times 4889560 (25.21%) aligned exactly 1 time 14307119 (73.77%) aligned >1 times 98.98% overall alignment rate Time searching: 00:12:43 Overall time: 00:12:43 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] 4563712 / 19196679 = 0.2377 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 14:25:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206505/SRX15206505.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206505/SRX15206505.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206505/SRX15206505.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206505/SRX15206505.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 14:25:22: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:25:22: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:25:30: 1000000 INFO @ Tue, 02 Aug 2022 14:25:38: 2000000 INFO @ Tue, 02 Aug 2022 14:25:47: 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 14:25:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206505/SRX15206505.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206505/SRX15206505.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206505/SRX15206505.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206505/SRX15206505.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 14:25:51: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:25:51: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:25:55: 4000000 INFO @ Tue, 02 Aug 2022 14:26:00: 1000000 INFO @ Tue, 02 Aug 2022 14:26:04: 5000000 INFO @ Tue, 02 Aug 2022 14:26:09: 2000000 INFO @ Tue, 02 Aug 2022 14:26:13: 6000000 INFO @ Tue, 02 Aug 2022 14:26:18: 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 14:26:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206505/SRX15206505.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206505/SRX15206505.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206505/SRX15206505.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206505/SRX15206505.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 14:26:21: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:26:21: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:26:22: 7000000 INFO @ Tue, 02 Aug 2022 14:26:27: 4000000 INFO @ Tue, 02 Aug 2022 14:26:29: 1000000 INFO @ Tue, 02 Aug 2022 14:26:31: 8000000 INFO @ Tue, 02 Aug 2022 14:26:36: 5000000 INFO @ Tue, 02 Aug 2022 14:26:37: 2000000 INFO @ Tue, 02 Aug 2022 14:26:40: 9000000 INFO @ Tue, 02 Aug 2022 14:26:44: 3000000 INFO @ Tue, 02 Aug 2022 14:26:45: 6000000 INFO @ Tue, 02 Aug 2022 14:26:49: 10000000 INFO @ Tue, 02 Aug 2022 14:26:52: 4000000 INFO @ Tue, 02 Aug 2022 14:26:53: 7000000 INFO @ Tue, 02 Aug 2022 14:26:58: 11000000 INFO @ Tue, 02 Aug 2022 14:27:00: 5000000 INFO @ Tue, 02 Aug 2022 14:27:02: 8000000 INFO @ Tue, 02 Aug 2022 14:27:06: 12000000 INFO @ Tue, 02 Aug 2022 14:27:07: 6000000 INFO @ Tue, 02 Aug 2022 14:27:10: 9000000 INFO @ Tue, 02 Aug 2022 14:27:14: 13000000 INFO @ Tue, 02 Aug 2022 14:27:15: 7000000 INFO @ Tue, 02 Aug 2022 14:27:19: 10000000 INFO @ Tue, 02 Aug 2022 14:27:22: 8000000 INFO @ Tue, 02 Aug 2022 14:27:22: 14000000 INFO @ Tue, 02 Aug 2022 14:27:27: 11000000 INFO @ Tue, 02 Aug 2022 14:27:28: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:27:28: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:27:28: #1 total tags in treatment: 14632967 INFO @ Tue, 02 Aug 2022 14:27:28: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:27:28: #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 14:27:28: #1 tags after filtering in treatment: 14632967 INFO @ Tue, 02 Aug 2022 14:27:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:27:28: #1 finished! INFO @ Tue, 02 Aug 2022 14:27:28: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:27:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:27:29: 9000000 INFO @ Tue, 02 Aug 2022 14:27:29: #2 number of paired peaks: 5642 INFO @ Tue, 02 Aug 2022 14:27:29: start model_add_line... INFO @ Tue, 02 Aug 2022 14:27:30: start X-correlation... INFO @ Tue, 02 Aug 2022 14:27:30: end of X-cor INFO @ Tue, 02 Aug 2022 14:27:30: #2 finished! INFO @ Tue, 02 Aug 2022 14:27:30: #2 predicted fragment length is 108 bps INFO @ Tue, 02 Aug 2022 14:27:30: #2 alternative fragment length(s) may be 4,108 bps INFO @ Tue, 02 Aug 2022 14:27:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206505/SRX15206505.05_model.r WARNING @ Tue, 02 Aug 2022 14:27:30: #2 Since the d (108) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:27:30: #2 You may need to consider one of the other alternative d(s): 4,108 WARNING @ Tue, 02 Aug 2022 14:27:30: #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 14:27:30: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:27:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:27:34: 12000000 INFO @ Tue, 02 Aug 2022 14:27:37: 10000000 INFO @ Tue, 02 Aug 2022 14:27:41: 13000000 INFO @ Tue, 02 Aug 2022 14:27:44: 11000000 INFO @ Tue, 02 Aug 2022 14:27:49: 14000000 INFO @ Tue, 02 Aug 2022 14:27:51: 12000000 INFO @ Tue, 02 Aug 2022 14:27:53: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:27:53: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:27:53: #1 total tags in treatment: 14632967 INFO @ Tue, 02 Aug 2022 14:27:53: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:27:53: #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 14:27:53: #1 tags after filtering in treatment: 14632967 INFO @ Tue, 02 Aug 2022 14:27:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:27:53: #1 finished! INFO @ Tue, 02 Aug 2022 14:27:53: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:27:53: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:27:55: #2 number of paired peaks: 5642 INFO @ Tue, 02 Aug 2022 14:27:55: start model_add_line... INFO @ Tue, 02 Aug 2022 14:27:55: start X-correlation... INFO @ Tue, 02 Aug 2022 14:27:55: end of X-cor INFO @ Tue, 02 Aug 2022 14:27:55: #2 finished! INFO @ Tue, 02 Aug 2022 14:27:55: #2 predicted fragment length is 108 bps INFO @ Tue, 02 Aug 2022 14:27:55: #2 alternative fragment length(s) may be 4,108 bps INFO @ Tue, 02 Aug 2022 14:27:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206505/SRX15206505.10_model.r WARNING @ Tue, 02 Aug 2022 14:27:55: #2 Since the d (108) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:27:55: #2 You may need to consider one of the other alternative d(s): 4,108 WARNING @ Tue, 02 Aug 2022 14:27:55: #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 14:27:55: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:27:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:27:58: 13000000 INFO @ Tue, 02 Aug 2022 14:28:05: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:28:07: 14000000 INFO @ Tue, 02 Aug 2022 14:28:12: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:28:12: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:28:12: #1 total tags in treatment: 14632967 INFO @ Tue, 02 Aug 2022 14:28:12: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:28:12: #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 14:28:12: #1 tags after filtering in treatment: 14632967 INFO @ Tue, 02 Aug 2022 14:28:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:28:12: #1 finished! INFO @ Tue, 02 Aug 2022 14:28:12: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:28:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:28:14: #2 number of paired peaks: 5642 INFO @ Tue, 02 Aug 2022 14:28:14: start model_add_line... INFO @ Tue, 02 Aug 2022 14:28:14: start X-correlation... INFO @ Tue, 02 Aug 2022 14:28:14: end of X-cor INFO @ Tue, 02 Aug 2022 14:28:14: #2 finished! INFO @ Tue, 02 Aug 2022 14:28:14: #2 predicted fragment length is 108 bps INFO @ Tue, 02 Aug 2022 14:28:14: #2 alternative fragment length(s) may be 4,108 bps INFO @ Tue, 02 Aug 2022 14:28:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206505/SRX15206505.20_model.r WARNING @ Tue, 02 Aug 2022 14:28:14: #2 Since the d (108) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:28:14: #2 You may need to consider one of the other alternative d(s): 4,108 WARNING @ Tue, 02 Aug 2022 14:28:14: #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 14:28:14: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:28:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:28:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206505/SRX15206505.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:28:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206505/SRX15206505.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:28:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206505/SRX15206505.05_summits.bed INFO @ Tue, 02 Aug 2022 14:28:20: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (17076 records, 4 fields): 50 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:28:29: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:28:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206505/SRX15206505.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:28:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206505/SRX15206505.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:28:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206505/SRX15206505.10_summits.bed INFO @ Tue, 02 Aug 2022 14:28:44: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (10015 records, 4 fields): 44 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:28:48: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:29:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206505/SRX15206505.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:29:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206505/SRX15206505.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:29:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206505/SRX15206505.20_summits.bed INFO @ Tue, 02 Aug 2022 14:29:02: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4301 records, 4 fields): 22 millis CompletedMACS2peakCalling