Job ID = 6627082 SRX = SRX8347288 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 17616780 spots for SRR11795471/SRR11795471.sra Written 17616780 spots for SRR11795471/SRR11795471.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627427 ("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: 00:53:12 17616780 reads; of these: 17616780 (100.00%) were paired; of these: 6625974 (37.61%) aligned concordantly 0 times 8242223 (46.79%) aligned concordantly exactly 1 time 2748583 (15.60%) aligned concordantly >1 times ---- 6625974 pairs aligned concordantly 0 times; of these: 950131 (14.34%) aligned discordantly 1 time ---- 5675843 pairs aligned 0 times concordantly or discordantly; of these: 11351686 mates make up the pairs; of these: 10360882 (91.27%) aligned 0 times 338588 (2.98%) aligned exactly 1 time 652216 (5.75%) aligned >1 times 70.59% overall alignment rate Time searching: 00:53:12 Overall time: 00:53:12 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 20 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 7448107 / 11890124 = 0.6264 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, 14 Jul 2020 10:50:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8347288/SRX8347288.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8347288/SRX8347288.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8347288/SRX8347288.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8347288/SRX8347288.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, 14 Jul 2020 10:50:29: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:50:29: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:50:37: 1000000 INFO @ Tue, 14 Jul 2020 10:50:45: 2000000 INFO @ Tue, 14 Jul 2020 10:50:53: 3000000 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, 14 Jul 2020 10:50:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8347288/SRX8347288.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8347288/SRX8347288.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8347288/SRX8347288.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8347288/SRX8347288.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, 14 Jul 2020 10:50:59: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:50:59: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:51:02: 4000000 INFO @ Tue, 14 Jul 2020 10:51:08: 1000000 INFO @ Tue, 14 Jul 2020 10:51:11: 5000000 INFO @ Tue, 14 Jul 2020 10:51:17: 2000000 INFO @ Tue, 14 Jul 2020 10:51:20: 6000000 INFO @ Tue, 14 Jul 2020 10:51:26: 3000000 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, 14 Jul 2020 10:51:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8347288/SRX8347288.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8347288/SRX8347288.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8347288/SRX8347288.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8347288/SRX8347288.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, 14 Jul 2020 10:51:29: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:51:29: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:51:29: 7000000 INFO @ Tue, 14 Jul 2020 10:51:36: 4000000 INFO @ Tue, 14 Jul 2020 10:51:39: 1000000 INFO @ Tue, 14 Jul 2020 10:51:40: 8000000 INFO @ Tue, 14 Jul 2020 10:51:47: 5000000 INFO @ Tue, 14 Jul 2020 10:51:49: 2000000 INFO @ Tue, 14 Jul 2020 10:51:51: 9000000 INFO @ Tue, 14 Jul 2020 10:51:57: 6000000 INFO @ Tue, 14 Jul 2020 10:52:00: 3000000 INFO @ Tue, 14 Jul 2020 10:52:00: #1 tag size is determined as 151 bps INFO @ Tue, 14 Jul 2020 10:52:00: #1 tag size = 151 INFO @ Tue, 14 Jul 2020 10:52:00: #1 total tags in treatment: 3973202 INFO @ Tue, 14 Jul 2020 10:52:00: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:52:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:52:00: #1 tags after filtering in treatment: 3804811 INFO @ Tue, 14 Jul 2020 10:52:00: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 14 Jul 2020 10:52:00: #1 finished! INFO @ Tue, 14 Jul 2020 10:52:00: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:52:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:52:01: #2 number of paired peaks: 1452 INFO @ Tue, 14 Jul 2020 10:52:01: start model_add_line... INFO @ Tue, 14 Jul 2020 10:52:01: start X-correlation... INFO @ Tue, 14 Jul 2020 10:52:01: end of X-cor INFO @ Tue, 14 Jul 2020 10:52:01: #2 finished! INFO @ Tue, 14 Jul 2020 10:52:01: #2 predicted fragment length is 241 bps INFO @ Tue, 14 Jul 2020 10:52:01: #2 alternative fragment length(s) may be 241 bps INFO @ Tue, 14 Jul 2020 10:52:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8347288/SRX8347288.05_model.r WARNING @ Tue, 14 Jul 2020 10:52:01: #2 Since the d (241) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:52:01: #2 You may need to consider one of the other alternative d(s): 241 WARNING @ Tue, 14 Jul 2020 10:52:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:52:01: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:52:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:52:07: 7000000 INFO @ Tue, 14 Jul 2020 10:52:09: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:52:09: 4000000 INFO @ Tue, 14 Jul 2020 10:52:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8347288/SRX8347288.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:52:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8347288/SRX8347288.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:52:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8347288/SRX8347288.05_summits.bed INFO @ Tue, 14 Jul 2020 10:52:14: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3961 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:52:16: 8000000 INFO @ Tue, 14 Jul 2020 10:52:19: 5000000 INFO @ Tue, 14 Jul 2020 10:52:26: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:52:29: 6000000 INFO @ Tue, 14 Jul 2020 10:52:36: #1 tag size is determined as 151 bps INFO @ Tue, 14 Jul 2020 10:52:36: #1 tag size = 151 INFO @ Tue, 14 Jul 2020 10:52:36: #1 total tags in treatment: 3973202 INFO @ Tue, 14 Jul 2020 10:52:36: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:52:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:52:36: #1 tags after filtering in treatment: 3804811 INFO @ Tue, 14 Jul 2020 10:52:36: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 14 Jul 2020 10:52:36: #1 finished! INFO @ Tue, 14 Jul 2020 10:52:36: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:52:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:52:36: #2 number of paired peaks: 1452 INFO @ Tue, 14 Jul 2020 10:52:36: start model_add_line... INFO @ Tue, 14 Jul 2020 10:52:36: start X-correlation... INFO @ Tue, 14 Jul 2020 10:52:36: end of X-cor INFO @ Tue, 14 Jul 2020 10:52:36: #2 finished! INFO @ Tue, 14 Jul 2020 10:52:36: #2 predicted fragment length is 241 bps INFO @ Tue, 14 Jul 2020 10:52:36: #2 alternative fragment length(s) may be 241 bps INFO @ Tue, 14 Jul 2020 10:52:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8347288/SRX8347288.10_model.r WARNING @ Tue, 14 Jul 2020 10:52:36: #2 Since the d (241) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:52:36: #2 You may need to consider one of the other alternative d(s): 241 WARNING @ Tue, 14 Jul 2020 10:52:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:52:36: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:52:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:52:38: 7000000 INFO @ Tue, 14 Jul 2020 10:52:45: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:52:48: 8000000 INFO @ Tue, 14 Jul 2020 10:52:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8347288/SRX8347288.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:52:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8347288/SRX8347288.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:52:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8347288/SRX8347288.10_summits.bed INFO @ Tue, 14 Jul 2020 10:52:49: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2428 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:52:57: 9000000 INFO @ Tue, 14 Jul 2020 10:53:05: #1 tag size is determined as 151 bps INFO @ Tue, 14 Jul 2020 10:53:05: #1 tag size = 151 INFO @ Tue, 14 Jul 2020 10:53:05: #1 total tags in treatment: 3973202 INFO @ Tue, 14 Jul 2020 10:53:05: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:53:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:53:06: #1 tags after filtering in treatment: 3804811 INFO @ Tue, 14 Jul 2020 10:53:06: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 14 Jul 2020 10:53:06: #1 finished! INFO @ Tue, 14 Jul 2020 10:53:06: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:53:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:53:06: #2 number of paired peaks: 1452 INFO @ Tue, 14 Jul 2020 10:53:06: start model_add_line... INFO @ Tue, 14 Jul 2020 10:53:06: start X-correlation... INFO @ Tue, 14 Jul 2020 10:53:06: end of X-cor INFO @ Tue, 14 Jul 2020 10:53:06: #2 finished! INFO @ Tue, 14 Jul 2020 10:53:06: #2 predicted fragment length is 241 bps INFO @ Tue, 14 Jul 2020 10:53:06: #2 alternative fragment length(s) may be 241 bps INFO @ Tue, 14 Jul 2020 10:53:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8347288/SRX8347288.20_model.r WARNING @ Tue, 14 Jul 2020 10:53:06: #2 Since the d (241) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:53:06: #2 You may need to consider one of the other alternative d(s): 241 WARNING @ Tue, 14 Jul 2020 10:53:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:53:06: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:53:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:53:15: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:53:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8347288/SRX8347288.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:53:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8347288/SRX8347288.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:53:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8347288/SRX8347288.20_summits.bed INFO @ Tue, 14 Jul 2020 10:53:19: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1070 records, 4 fields): 3 millis CompletedMACS2peakCalling