Job ID = 14167492 SRX = SRX7723690 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: 00:02:57 9112030 reads; of these: 9112030 (100.00%) were unpaired; of these: 1000096 (10.98%) aligned 0 times 5746100 (63.06%) aligned exactly 1 time 2365834 (25.96%) aligned >1 times 89.02% overall alignment rate Time searching: 00:02:57 Overall time: 00:02:57 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_rmdupse_core] 989608 / 8111934 = 0.1220 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 12:31:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7723690/SRX7723690.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7723690/SRX7723690.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7723690/SRX7723690.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7723690/SRX7723690.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 @ Fri, 10 Dec 2021 12:31:46: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:31:46: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:31:52: 1000000 INFO @ Fri, 10 Dec 2021 12:31:57: 2000000 INFO @ Fri, 10 Dec 2021 12:32:02: 3000000 INFO @ Fri, 10 Dec 2021 12:32:07: 4000000 INFO @ Fri, 10 Dec 2021 12:32:13: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 12:32:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7723690/SRX7723690.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7723690/SRX7723690.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7723690/SRX7723690.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7723690/SRX7723690.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 @ Fri, 10 Dec 2021 12:32:16: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:32:16: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:32:18: 6000000 INFO @ Fri, 10 Dec 2021 12:32:22: 1000000 INFO @ Fri, 10 Dec 2021 12:32:24: 7000000 INFO @ Fri, 10 Dec 2021 12:32:25: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 12:32:25: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 12:32:25: #1 total tags in treatment: 7122326 INFO @ Fri, 10 Dec 2021 12:32:25: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:32:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 12:32:25: #1 tags after filtering in treatment: 7122103 INFO @ Fri, 10 Dec 2021 12:32:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:32:25: #1 finished! INFO @ Fri, 10 Dec 2021 12:32:25: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:32:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:32:26: #2 number of paired peaks: 2038 INFO @ Fri, 10 Dec 2021 12:32:26: start model_add_line... INFO @ Fri, 10 Dec 2021 12:32:26: start X-correlation... INFO @ Fri, 10 Dec 2021 12:32:26: end of X-cor INFO @ Fri, 10 Dec 2021 12:32:26: #2 finished! INFO @ Fri, 10 Dec 2021 12:32:26: #2 predicted fragment length is 98 bps INFO @ Fri, 10 Dec 2021 12:32:26: #2 alternative fragment length(s) may be 98 bps INFO @ Fri, 10 Dec 2021 12:32:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7723690/SRX7723690.05_model.r INFO @ Fri, 10 Dec 2021 12:32:27: 2000000 WARNING @ Fri, 10 Dec 2021 12:32:28: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:32:28: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Fri, 10 Dec 2021 12:32:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 12:32:28: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:32:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:32:33: 3000000 INFO @ Fri, 10 Dec 2021 12:32:38: 4000000 INFO @ Fri, 10 Dec 2021 12:32:42: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:32:44: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 12:32:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7723690/SRX7723690.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7723690/SRX7723690.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7723690/SRX7723690.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7723690/SRX7723690.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 @ Fri, 10 Dec 2021 12:32:46: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:32:46: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:32:49: 6000000 INFO @ Fri, 10 Dec 2021 12:32:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7723690/SRX7723690.05_peaks.xls INFO @ Fri, 10 Dec 2021 12:32:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7723690/SRX7723690.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:32:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7723690/SRX7723690.05_summits.bed INFO @ Fri, 10 Dec 2021 12:32:50: Done! pass1 - making usageList (505 chroms): 2 millis pass2 - checking and writing primary data (2747 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:32:53: 1000000 INFO @ Fri, 10 Dec 2021 12:32:55: 7000000 INFO @ Fri, 10 Dec 2021 12:32:56: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 12:32:56: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 12:32:56: #1 total tags in treatment: 7122326 INFO @ Fri, 10 Dec 2021 12:32:56: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:32:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 12:32:56: #1 tags after filtering in treatment: 7122103 INFO @ Fri, 10 Dec 2021 12:32:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:32:56: #1 finished! INFO @ Fri, 10 Dec 2021 12:32:56: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:32:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:32:57: #2 number of paired peaks: 2038 INFO @ Fri, 10 Dec 2021 12:32:57: start model_add_line... INFO @ Fri, 10 Dec 2021 12:32:57: start X-correlation... INFO @ Fri, 10 Dec 2021 12:32:57: end of X-cor INFO @ Fri, 10 Dec 2021 12:32:57: #2 finished! INFO @ Fri, 10 Dec 2021 12:32:57: #2 predicted fragment length is 98 bps INFO @ Fri, 10 Dec 2021 12:32:57: #2 alternative fragment length(s) may be 98 bps INFO @ Fri, 10 Dec 2021 12:32:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7723690/SRX7723690.10_model.r WARNING @ Fri, 10 Dec 2021 12:32:57: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:32:57: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Fri, 10 Dec 2021 12:32:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 12:32:57: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:32:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:33:00: 2000000 INFO @ Fri, 10 Dec 2021 12:33:06: 3000000 INFO @ Fri, 10 Dec 2021 12:33:12: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:33:13: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 12:33:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7723690/SRX7723690.10_peaks.xls INFO @ Fri, 10 Dec 2021 12:33:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7723690/SRX7723690.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:33:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7723690/SRX7723690.10_summits.bed INFO @ Fri, 10 Dec 2021 12:33:19: 5000000 INFO @ Fri, 10 Dec 2021 12:33:19: Done! pass1 - making usageList (349 chroms): 1 millis pass2 - checking and writing primary data (1243 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:33:26: 6000000 INFO @ Fri, 10 Dec 2021 12:33:33: 7000000 INFO @ Fri, 10 Dec 2021 12:33:33: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 12:33:33: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 12:33:33: #1 total tags in treatment: 7122326 INFO @ Fri, 10 Dec 2021 12:33:33: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:33:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 12:33:34: #1 tags after filtering in treatment: 7122103 INFO @ Fri, 10 Dec 2021 12:33:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:33:34: #1 finished! INFO @ Fri, 10 Dec 2021 12:33:34: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:33:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:33:34: #2 number of paired peaks: 2038 INFO @ Fri, 10 Dec 2021 12:33:34: start model_add_line... INFO @ Fri, 10 Dec 2021 12:33:34: start X-correlation... INFO @ Fri, 10 Dec 2021 12:33:34: end of X-cor INFO @ Fri, 10 Dec 2021 12:33:34: #2 finished! INFO @ Fri, 10 Dec 2021 12:33:34: #2 predicted fragment length is 98 bps INFO @ Fri, 10 Dec 2021 12:33:34: #2 alternative fragment length(s) may be 98 bps INFO @ Fri, 10 Dec 2021 12:33:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7723690/SRX7723690.20_model.r WARNING @ Fri, 10 Dec 2021 12:33:34: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:33:34: #2 You may need to consider one of the other alternative d(s): 98 WARNING @ Fri, 10 Dec 2021 12:33:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 12:33:34: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:33:34: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 12:33:50: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:33:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7723690/SRX7723690.20_peaks.xls INFO @ Fri, 10 Dec 2021 12:33:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7723690/SRX7723690.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:33:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7723690/SRX7723690.20_summits.bed INFO @ Fri, 10 Dec 2021 12:33:57: Done! pass1 - making usageList (245 chroms): 1 millis pass2 - checking and writing primary data (660 records, 4 fields): 9 millis CompletedMACS2peakCalling