Job ID = 6529165 SRX = SRX025466 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: 00:21:40 58341165 reads; of these: 58341165 (100.00%) were unpaired; of these: 5360220 (9.19%) aligned 0 times 19208037 (32.92%) aligned exactly 1 time 33772908 (57.89%) aligned >1 times 90.81% overall alignment rate Time searching: 00:21:40 Overall time: 00:21:40 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 16 files... [bam_rmdupse_core] 42673926 / 52980945 = 0.8055 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 01:56:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX025466/SRX025466.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX025466/SRX025466.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX025466/SRX025466.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX025466/SRX025466.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, 30 Jun 2020 01:56:09: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:56:09: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:56:14: 1000000 INFO @ Tue, 30 Jun 2020 01:56:20: 2000000 INFO @ Tue, 30 Jun 2020 01:56:25: 3000000 INFO @ Tue, 30 Jun 2020 01:56:31: 4000000 INFO @ Tue, 30 Jun 2020 01:56:36: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 01:56:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX025466/SRX025466.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX025466/SRX025466.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX025466/SRX025466.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX025466/SRX025466.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, 30 Jun 2020 01:56:40: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:56:40: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:56:42: 6000000 INFO @ Tue, 30 Jun 2020 01:56:45: 1000000 INFO @ Tue, 30 Jun 2020 01:56:48: 7000000 INFO @ Tue, 30 Jun 2020 01:56:50: 2000000 INFO @ Tue, 30 Jun 2020 01:56:54: 8000000 INFO @ Tue, 30 Jun 2020 01:56:56: 3000000 INFO @ Tue, 30 Jun 2020 01:57:00: 9000000 INFO @ Tue, 30 Jun 2020 01:57:01: 4000000 INFO @ Tue, 30 Jun 2020 01:57:06: 10000000 INFO @ Tue, 30 Jun 2020 01:57:06: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 01:57:07: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:57:07: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:57:07: #1 total tags in treatment: 10307019 INFO @ Tue, 30 Jun 2020 01:57:07: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:57:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:57:08: #1 tags after filtering in treatment: 10307017 INFO @ Tue, 30 Jun 2020 01:57:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:57:08: #1 finished! INFO @ Tue, 30 Jun 2020 01:57:08: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:57:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:57:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX025466/SRX025466.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX025466/SRX025466.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX025466/SRX025466.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX025466/SRX025466.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, 30 Jun 2020 01:57:09: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:57:09: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:57:09: #2 number of paired peaks: 7780 INFO @ Tue, 30 Jun 2020 01:57:09: start model_add_line... INFO @ Tue, 30 Jun 2020 01:57:09: start X-correlation... INFO @ Tue, 30 Jun 2020 01:57:10: end of X-cor INFO @ Tue, 30 Jun 2020 01:57:10: #2 finished! INFO @ Tue, 30 Jun 2020 01:57:10: #2 predicted fragment length is 38 bps INFO @ Tue, 30 Jun 2020 01:57:10: #2 alternative fragment length(s) may be 2,38 bps INFO @ Tue, 30 Jun 2020 01:57:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX025466/SRX025466.05_model.r WARNING @ Tue, 30 Jun 2020 01:57:10: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:57:10: #2 You may need to consider one of the other alternative d(s): 2,38 WARNING @ Tue, 30 Jun 2020 01:57:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:57:10: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:57:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:57:12: 6000000 INFO @ Tue, 30 Jun 2020 01:57:14: 1000000 INFO @ Tue, 30 Jun 2020 01:57:17: 7000000 INFO @ Tue, 30 Jun 2020 01:57:20: 2000000 INFO @ Tue, 30 Jun 2020 01:57:23: 8000000 INFO @ Tue, 30 Jun 2020 01:57:25: 3000000 INFO @ Tue, 30 Jun 2020 01:57:28: 9000000 INFO @ Tue, 30 Jun 2020 01:57:30: 4000000 INFO @ Tue, 30 Jun 2020 01:57:31: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:57:33: 10000000 INFO @ Tue, 30 Jun 2020 01:57:35: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:57:35: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:57:35: #1 total tags in treatment: 10307019 INFO @ Tue, 30 Jun 2020 01:57:35: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:57:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:57:35: #1 tags after filtering in treatment: 10307017 INFO @ Tue, 30 Jun 2020 01:57:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:57:35: #1 finished! INFO @ Tue, 30 Jun 2020 01:57:35: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:57:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:57:36: 5000000 INFO @ Tue, 30 Jun 2020 01:57:37: #2 number of paired peaks: 7780 INFO @ Tue, 30 Jun 2020 01:57:37: start model_add_line... INFO @ Tue, 30 Jun 2020 01:57:37: start X-correlation... INFO @ Tue, 30 Jun 2020 01:57:37: end of X-cor INFO @ Tue, 30 Jun 2020 01:57:37: #2 finished! INFO @ Tue, 30 Jun 2020 01:57:37: #2 predicted fragment length is 38 bps INFO @ Tue, 30 Jun 2020 01:57:37: #2 alternative fragment length(s) may be 2,38 bps INFO @ Tue, 30 Jun 2020 01:57:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX025466/SRX025466.10_model.r WARNING @ Tue, 30 Jun 2020 01:57:37: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:57:37: #2 You may need to consider one of the other alternative d(s): 2,38 WARNING @ Tue, 30 Jun 2020 01:57:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:57:37: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:57:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:57:41: 6000000 INFO @ Tue, 30 Jun 2020 01:57:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX025466/SRX025466.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:57:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX025466/SRX025466.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:57:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX025466/SRX025466.05_summits.bed INFO @ Tue, 30 Jun 2020 01:57:42: Done! pass1 - making usageList (1145 chroms): 2 millis pass2 - checking and writing primary data (8752 records, 4 fields): 40 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:57:46: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:57:51: 8000000 INFO @ Tue, 30 Jun 2020 01:57:56: 9000000 INFO @ Tue, 30 Jun 2020 01:57:59: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:58:01: 10000000 INFO @ Tue, 30 Jun 2020 01:58:03: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:58:03: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:58:03: #1 total tags in treatment: 10307019 INFO @ Tue, 30 Jun 2020 01:58:03: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:58:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:58:03: #1 tags after filtering in treatment: 10307017 INFO @ Tue, 30 Jun 2020 01:58:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:58:03: #1 finished! INFO @ Tue, 30 Jun 2020 01:58:03: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:58:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:58:05: #2 number of paired peaks: 7780 INFO @ Tue, 30 Jun 2020 01:58:05: start model_add_line... INFO @ Tue, 30 Jun 2020 01:58:05: start X-correlation... INFO @ Tue, 30 Jun 2020 01:58:05: end of X-cor INFO @ Tue, 30 Jun 2020 01:58:05: #2 finished! INFO @ Tue, 30 Jun 2020 01:58:05: #2 predicted fragment length is 38 bps INFO @ Tue, 30 Jun 2020 01:58:05: #2 alternative fragment length(s) may be 2,38 bps INFO @ Tue, 30 Jun 2020 01:58:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX025466/SRX025466.20_model.r WARNING @ Tue, 30 Jun 2020 01:58:05: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:58:05: #2 You may need to consider one of the other alternative d(s): 2,38 WARNING @ Tue, 30 Jun 2020 01:58:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:58:05: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:58:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:58:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX025466/SRX025466.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:58:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX025466/SRX025466.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:58:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX025466/SRX025466.10_summits.bed INFO @ Tue, 30 Jun 2020 01:58:10: Done! pass1 - making usageList (945 chroms): 2 millis pass2 - checking and writing primary data (4907 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:58:25: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:58:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX025466/SRX025466.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:58:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX025466/SRX025466.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:58:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX025466/SRX025466.20_summits.bed INFO @ Tue, 30 Jun 2020 01:58:35: Done! pass1 - making usageList (682 chroms): 1 millis pass2 - checking and writing primary data (2834 records, 4 fields): 22 millis CompletedMACS2peakCalling