Job ID = 6626572 SRX = SRX7224574 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 13032527 spots for SRR10541130/SRR10541130.sra Written 13032527 spots for SRR10541130/SRR10541130.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626740 ("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: 00:23:49 13032527 reads; of these: 13032527 (100.00%) were paired; of these: 3682300 (28.25%) aligned concordantly 0 times 8515978 (65.34%) aligned concordantly exactly 1 time 834249 (6.40%) aligned concordantly >1 times ---- 3682300 pairs aligned concordantly 0 times; of these: 2391299 (64.94%) aligned discordantly 1 time ---- 1291001 pairs aligned 0 times concordantly or discordantly; of these: 2582002 mates make up the pairs; of these: 1753830 (67.93%) aligned 0 times 329343 (12.76%) aligned exactly 1 time 498829 (19.32%) aligned >1 times 93.27% overall alignment rate Time searching: 00:23:49 Overall time: 00:23:49 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] 2039379 / 11483931 = 0.1776 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 08:09:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7224574/SRX7224574.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7224574/SRX7224574.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7224574/SRX7224574.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7224574/SRX7224574.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 08:09:26: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:09:26: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:09:33: 1000000 INFO @ Tue, 14 Jul 2020 08:09:40: 2000000 INFO @ Tue, 14 Jul 2020 08:09:47: 3000000 INFO @ Tue, 14 Jul 2020 08:09:54: 4000000 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 08:09:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7224574/SRX7224574.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7224574/SRX7224574.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7224574/SRX7224574.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7224574/SRX7224574.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 08:09:57: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:09:57: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:10:01: 5000000 INFO @ Tue, 14 Jul 2020 08:10:06: 1000000 INFO @ Tue, 14 Jul 2020 08:10:09: 6000000 INFO @ Tue, 14 Jul 2020 08:10:15: 2000000 INFO @ Tue, 14 Jul 2020 08:10:16: 7000000 INFO @ Tue, 14 Jul 2020 08:10:24: 8000000 INFO @ Tue, 14 Jul 2020 08:10:24: 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 08:10:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7224574/SRX7224574.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7224574/SRX7224574.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7224574/SRX7224574.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7224574/SRX7224574.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 08:10:26: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:10:26: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:10:32: 9000000 INFO @ Tue, 14 Jul 2020 08:10:34: 4000000 INFO @ Tue, 14 Jul 2020 08:10:35: 1000000 INFO @ Tue, 14 Jul 2020 08:10:40: 10000000 INFO @ Tue, 14 Jul 2020 08:10:43: 2000000 INFO @ Tue, 14 Jul 2020 08:10:43: 5000000 INFO @ Tue, 14 Jul 2020 08:10:48: 11000000 INFO @ Tue, 14 Jul 2020 08:10:51: 3000000 INFO @ Tue, 14 Jul 2020 08:10:53: 6000000 INFO @ Tue, 14 Jul 2020 08:10:56: 12000000 INFO @ Tue, 14 Jul 2020 08:10:59: 4000000 INFO @ Tue, 14 Jul 2020 08:11:02: 7000000 INFO @ Tue, 14 Jul 2020 08:11:04: 13000000 INFO @ Tue, 14 Jul 2020 08:11:07: 5000000 INFO @ Tue, 14 Jul 2020 08:11:12: 8000000 INFO @ Tue, 14 Jul 2020 08:11:13: 14000000 INFO @ Tue, 14 Jul 2020 08:11:15: 6000000 INFO @ Tue, 14 Jul 2020 08:11:21: 15000000 INFO @ Tue, 14 Jul 2020 08:11:21: 9000000 INFO @ Tue, 14 Jul 2020 08:11:23: 7000000 INFO @ Tue, 14 Jul 2020 08:11:29: 16000000 INFO @ Tue, 14 Jul 2020 08:11:31: 10000000 INFO @ Tue, 14 Jul 2020 08:11:31: 8000000 INFO @ Tue, 14 Jul 2020 08:11:37: 17000000 INFO @ Tue, 14 Jul 2020 08:11:39: 9000000 INFO @ Tue, 14 Jul 2020 08:11:40: 11000000 INFO @ Tue, 14 Jul 2020 08:11:45: 18000000 INFO @ Tue, 14 Jul 2020 08:11:47: 10000000 INFO @ Tue, 14 Jul 2020 08:11:49: 12000000 INFO @ Tue, 14 Jul 2020 08:11:54: 19000000 INFO @ Tue, 14 Jul 2020 08:11:55: 11000000 INFO @ Tue, 14 Jul 2020 08:11:59: 13000000 INFO @ Tue, 14 Jul 2020 08:12:02: 20000000 INFO @ Tue, 14 Jul 2020 08:12:03: 12000000 INFO @ Tue, 14 Jul 2020 08:12:04: #1 tag size is determined as 150 bps INFO @ Tue, 14 Jul 2020 08:12:04: #1 tag size = 150 INFO @ Tue, 14 Jul 2020 08:12:04: #1 total tags in treatment: 7649186 INFO @ Tue, 14 Jul 2020 08:12:04: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:12:04: #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 08:12:04: #1 tags after filtering in treatment: 6521478 INFO @ Tue, 14 Jul 2020 08:12:04: #1 Redundant rate of treatment: 0.15 INFO @ Tue, 14 Jul 2020 08:12:04: #1 finished! INFO @ Tue, 14 Jul 2020 08:12:04: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:12:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:12:05: #2 number of paired peaks: 13352 INFO @ Tue, 14 Jul 2020 08:12:05: start model_add_line... INFO @ Tue, 14 Jul 2020 08:12:05: start X-correlation... INFO @ Tue, 14 Jul 2020 08:12:05: end of X-cor INFO @ Tue, 14 Jul 2020 08:12:05: #2 finished! INFO @ Tue, 14 Jul 2020 08:12:05: #2 predicted fragment length is 171 bps INFO @ Tue, 14 Jul 2020 08:12:05: #2 alternative fragment length(s) may be 171 bps INFO @ Tue, 14 Jul 2020 08:12:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7224574/SRX7224574.05_model.r WARNING @ Tue, 14 Jul 2020 08:12:05: #2 Since the d (171) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:12:05: #2 You may need to consider one of the other alternative d(s): 171 WARNING @ Tue, 14 Jul 2020 08:12:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:12:05: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:12:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:12:08: 14000000 INFO @ Tue, 14 Jul 2020 08:12:11: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 08:12:18: 15000000 INFO @ Tue, 14 Jul 2020 08:12:19: 14000000 INFO @ Tue, 14 Jul 2020 08:12:21: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:12:26: 15000000 INFO @ Tue, 14 Jul 2020 08:12:27: 16000000 INFO @ Tue, 14 Jul 2020 08:12:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7224574/SRX7224574.05_peaks.xls INFO @ Tue, 14 Jul 2020 08:12:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7224574/SRX7224574.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:12:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7224574/SRX7224574.05_summits.bed INFO @ Tue, 14 Jul 2020 08:12:28: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8599 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:12:34: 16000000 INFO @ Tue, 14 Jul 2020 08:12:37: 17000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 08:12:42: 17000000 INFO @ Tue, 14 Jul 2020 08:12:46: 18000000 INFO @ Tue, 14 Jul 2020 08:12:50: 18000000 INFO @ Tue, 14 Jul 2020 08:12:55: 19000000 INFO @ Tue, 14 Jul 2020 08:12:59: 19000000 INFO @ Tue, 14 Jul 2020 08:13:04: 20000000 INFO @ Tue, 14 Jul 2020 08:13:06: #1 tag size is determined as 150 bps INFO @ Tue, 14 Jul 2020 08:13:06: #1 tag size = 150 INFO @ Tue, 14 Jul 2020 08:13:06: #1 total tags in treatment: 7649186 INFO @ Tue, 14 Jul 2020 08:13:06: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:13:06: #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 08:13:06: #1 tags after filtering in treatment: 6521478 INFO @ Tue, 14 Jul 2020 08:13:06: #1 Redundant rate of treatment: 0.15 INFO @ Tue, 14 Jul 2020 08:13:06: #1 finished! INFO @ Tue, 14 Jul 2020 08:13:06: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:13:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:13:07: 20000000 INFO @ Tue, 14 Jul 2020 08:13:07: #2 number of paired peaks: 13352 INFO @ Tue, 14 Jul 2020 08:13:07: start model_add_line... INFO @ Tue, 14 Jul 2020 08:13:08: start X-correlation... INFO @ Tue, 14 Jul 2020 08:13:08: end of X-cor INFO @ Tue, 14 Jul 2020 08:13:08: #2 finished! INFO @ Tue, 14 Jul 2020 08:13:08: #2 predicted fragment length is 171 bps INFO @ Tue, 14 Jul 2020 08:13:08: #2 alternative fragment length(s) may be 171 bps INFO @ Tue, 14 Jul 2020 08:13:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7224574/SRX7224574.10_model.r WARNING @ Tue, 14 Jul 2020 08:13:08: #2 Since the d (171) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:13:08: #2 You may need to consider one of the other alternative d(s): 171 WARNING @ Tue, 14 Jul 2020 08:13:08: #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 08:13:08: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:13:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:13:08: #1 tag size is determined as 150 bps INFO @ Tue, 14 Jul 2020 08:13:08: #1 tag size = 150 INFO @ Tue, 14 Jul 2020 08:13:08: #1 total tags in treatment: 7649186 INFO @ Tue, 14 Jul 2020 08:13:08: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:13:08: #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 08:13:09: #1 tags after filtering in treatment: 6521478 INFO @ Tue, 14 Jul 2020 08:13:09: #1 Redundant rate of treatment: 0.15 INFO @ Tue, 14 Jul 2020 08:13:09: #1 finished! INFO @ Tue, 14 Jul 2020 08:13:09: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:13:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:13:10: #2 number of paired peaks: 13352 INFO @ Tue, 14 Jul 2020 08:13:10: start model_add_line... INFO @ Tue, 14 Jul 2020 08:13:10: start X-correlation... INFO @ Tue, 14 Jul 2020 08:13:10: end of X-cor INFO @ Tue, 14 Jul 2020 08:13:10: #2 finished! INFO @ Tue, 14 Jul 2020 08:13:10: #2 predicted fragment length is 171 bps INFO @ Tue, 14 Jul 2020 08:13:10: #2 alternative fragment length(s) may be 171 bps INFO @ Tue, 14 Jul 2020 08:13:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7224574/SRX7224574.20_model.r WARNING @ Tue, 14 Jul 2020 08:13:10: #2 Since the d (171) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:13:10: #2 You may need to consider one of the other alternative d(s): 171 WARNING @ Tue, 14 Jul 2020 08:13:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:13:10: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:13:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:13:23: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:13:26: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:13:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7224574/SRX7224574.10_peaks.xls INFO @ Tue, 14 Jul 2020 08:13:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7224574/SRX7224574.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:13:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7224574/SRX7224574.10_summits.bed INFO @ Tue, 14 Jul 2020 08:13:31: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (7816 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:13:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7224574/SRX7224574.20_peaks.xls INFO @ Tue, 14 Jul 2020 08:13:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7224574/SRX7224574.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:13:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7224574/SRX7224574.20_summits.bed INFO @ Tue, 14 Jul 2020 08:13:33: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (6429 records, 4 fields): 7 millis CompletedMACS2peakCalling