Job ID = 16439019 SRX = SRX15206521 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:57 18246254 reads; of these: 18246254 (100.00%) were unpaired; of these: 1101563 (6.04%) aligned 0 times 12477308 (68.38%) aligned exactly 1 time 4667383 (25.58%) aligned >1 times 93.96% overall alignment rate Time searching: 00:05:58 Overall time: 00:05:58 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 9095322 / 17144691 = 0.5305 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 14:35:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206521/SRX15206521.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206521/SRX15206521.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206521/SRX15206521.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/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 14:35:11: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:35:11: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:35:19: 1000000 INFO @ Tue, 02 Aug 2022 14:35:27: 2000000 INFO @ Tue, 02 Aug 2022 14:35:35: 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 14:35:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206521/SRX15206521.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206521/SRX15206521.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206521/SRX15206521.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/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 14:35:41: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:35:41: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:35:43: 4000000 INFO @ Tue, 02 Aug 2022 14:35:49: 1000000 INFO @ Tue, 02 Aug 2022 14:35:52: 5000000 INFO @ Tue, 02 Aug 2022 14:35:57: 2000000 INFO @ Tue, 02 Aug 2022 14:36:01: 6000000 INFO @ Tue, 02 Aug 2022 14:36:04: 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 14:36:10: 7000000 INFO @ Tue, 02 Aug 2022 14:36:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206521/SRX15206521.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206521/SRX15206521.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206521/SRX15206521.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/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 14:36:11: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:36:11: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:36:12: 4000000 INFO @ Tue, 02 Aug 2022 14:36:19: 8000000 INFO @ Tue, 02 Aug 2022 14:36:19: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:36:19: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:36:19: #1 total tags in treatment: 8049369 INFO @ Tue, 02 Aug 2022 14:36:19: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:36:19: #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 14:36:19: 1000000 INFO @ Tue, 02 Aug 2022 14:36:19: #1 tags after filtering in treatment: 8049241 INFO @ Tue, 02 Aug 2022 14:36:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:36:19: #1 finished! INFO @ Tue, 02 Aug 2022 14:36:19: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:36:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:36:20: 5000000 INFO @ Tue, 02 Aug 2022 14:36:20: #2 number of paired peaks: 2857 INFO @ Tue, 02 Aug 2022 14:36:20: start model_add_line... INFO @ Tue, 02 Aug 2022 14:36:20: start X-correlation... INFO @ Tue, 02 Aug 2022 14:36:20: end of X-cor INFO @ Tue, 02 Aug 2022 14:36:20: #2 finished! INFO @ Tue, 02 Aug 2022 14:36:20: #2 predicted fragment length is 134 bps INFO @ Tue, 02 Aug 2022 14:36:20: #2 alternative fragment length(s) may be 134 bps INFO @ Tue, 02 Aug 2022 14:36:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206521/SRX15206521.05_model.r WARNING @ Tue, 02 Aug 2022 14:36:20: #2 Since the d (134) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:36:20: #2 You may need to consider one of the other alternative d(s): 134 WARNING @ Tue, 02 Aug 2022 14:36:20: #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 14:36:20: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:36:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:36:26: 2000000 INFO @ Tue, 02 Aug 2022 14:36:27: 6000000 INFO @ Tue, 02 Aug 2022 14:36:33: 3000000 INFO @ Tue, 02 Aug 2022 14:36:33: 7000000 INFO @ Tue, 02 Aug 2022 14:36:39: 4000000 INFO @ Tue, 02 Aug 2022 14:36:40: 8000000 INFO @ Tue, 02 Aug 2022 14:36:40: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:36:40: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:36:40: #1 total tags in treatment: 8049369 INFO @ Tue, 02 Aug 2022 14:36:40: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:36:40: #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 14:36:40: #1 tags after filtering in treatment: 8049241 INFO @ Tue, 02 Aug 2022 14:36:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:36:40: #1 finished! INFO @ Tue, 02 Aug 2022 14:36:40: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:36:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:36:41: #2 number of paired peaks: 2857 INFO @ Tue, 02 Aug 2022 14:36:41: start model_add_line... INFO @ Tue, 02 Aug 2022 14:36:41: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:36:41: start X-correlation... INFO @ Tue, 02 Aug 2022 14:36:41: end of X-cor INFO @ Tue, 02 Aug 2022 14:36:41: #2 finished! INFO @ Tue, 02 Aug 2022 14:36:41: #2 predicted fragment length is 134 bps INFO @ Tue, 02 Aug 2022 14:36:41: #2 alternative fragment length(s) may be 134 bps INFO @ Tue, 02 Aug 2022 14:36:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206521/SRX15206521.10_model.r WARNING @ Tue, 02 Aug 2022 14:36:41: #2 Since the d (134) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:36:41: #2 You may need to consider one of the other alternative d(s): 134 WARNING @ Tue, 02 Aug 2022 14:36:41: #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 14:36:41: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:36:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:36:45: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:36:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206521/SRX15206521.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:36:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206521/SRX15206521.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:36:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206521/SRX15206521.05_summits.bed INFO @ Tue, 02 Aug 2022 14:36:51: Done! INFO @ Tue, 02 Aug 2022 14:36:51: 6000000 pass1 - making usageList (392 chroms): 2 millis pass2 - checking and writing primary data (5736 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:36:58: 7000000 INFO @ Tue, 02 Aug 2022 14:37:01: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:37:04: 8000000 INFO @ Tue, 02 Aug 2022 14:37:04: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:37:04: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:37:04: #1 total tags in treatment: 8049369 INFO @ Tue, 02 Aug 2022 14:37:04: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:37:04: #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 14:37:04: #1 tags after filtering in treatment: 8049241 INFO @ Tue, 02 Aug 2022 14:37:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:37:04: #1 finished! INFO @ Tue, 02 Aug 2022 14:37:04: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:37:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:37:05: #2 number of paired peaks: 2857 INFO @ Tue, 02 Aug 2022 14:37:05: start model_add_line... INFO @ Tue, 02 Aug 2022 14:37:05: start X-correlation... INFO @ Tue, 02 Aug 2022 14:37:05: end of X-cor INFO @ Tue, 02 Aug 2022 14:37:05: #2 finished! INFO @ Tue, 02 Aug 2022 14:37:05: #2 predicted fragment length is 134 bps INFO @ Tue, 02 Aug 2022 14:37:05: #2 alternative fragment length(s) may be 134 bps INFO @ Tue, 02 Aug 2022 14:37:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206521/SRX15206521.20_model.r WARNING @ Tue, 02 Aug 2022 14:37:05: #2 Since the d (134) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:37:05: #2 You may need to consider one of the other alternative d(s): 134 WARNING @ Tue, 02 Aug 2022 14:37:05: #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 14:37:05: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:37:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:37:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206521/SRX15206521.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:37:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206521/SRX15206521.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:37:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206521/SRX15206521.10_summits.bed INFO @ Tue, 02 Aug 2022 14:37:11: Done! pass1 - making usageList (327 chroms): 1 millis pass2 - checking and writing primary data (3280 records, 4 fields): 145 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:37:26: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:37:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206521/SRX15206521.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:37:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206521/SRX15206521.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:37:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206521/SRX15206521.20_summits.bed INFO @ Tue, 02 Aug 2022 14:37:35: Done! pass1 - making usageList (265 chroms): 1 millis pass2 - checking and writing primary data (1747 records, 4 fields): 31 millis CompletedMACS2peakCalling