Job ID = 6627062 SRX = SRX8347277 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-14T00:41:59 prefetch.2.10.7: 1) Downloading 'SRR11795460'... 2020-07-14T00:41:59 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T00:47:04 prefetch.2.10.7: HTTPS download succeed 2020-07-14T00:47:04 prefetch.2.10.7: 1) 'SRR11795460' was downloaded successfully 2020-07-14T00:47:04 prefetch.2.10.7: 'SRR11795460' has 0 unresolved dependencies Read 14999327 spots for SRR11795460/SRR11795460.sra Written 14999327 spots for SRR11795460/SRR11795460.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627403 ("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: 00:44:29 14999327 reads; of these: 14999327 (100.00%) were paired; of these: 4548464 (30.32%) aligned concordantly 0 times 8334670 (55.57%) aligned concordantly exactly 1 time 2116193 (14.11%) aligned concordantly >1 times ---- 4548464 pairs aligned concordantly 0 times; of these: 798845 (17.56%) aligned discordantly 1 time ---- 3749619 pairs aligned 0 times concordantly or discordantly; of these: 7499238 mates make up the pairs; of these: 6709252 (89.47%) aligned 0 times 320802 (4.28%) aligned exactly 1 time 469184 (6.26%) aligned >1 times 77.63% overall alignment rate Time searching: 00:44:29 Overall time: 00:44:29 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] 6237341 / 11207749 = 0.5565 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 10:41:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8347277/SRX8347277.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8347277/SRX8347277.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8347277/SRX8347277.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8347277/SRX8347277.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 10:41:57: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:41:57: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:42:05: 1000000 INFO @ Tue, 14 Jul 2020 10:42:13: 2000000 INFO @ Tue, 14 Jul 2020 10:42:21: 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 10:42:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8347277/SRX8347277.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8347277/SRX8347277.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8347277/SRX8347277.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8347277/SRX8347277.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 10:42:27: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:42:27: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:42:29: 4000000 INFO @ Tue, 14 Jul 2020 10:42:36: 1000000 INFO @ Tue, 14 Jul 2020 10:42:38: 5000000 INFO @ Tue, 14 Jul 2020 10:42:45: 2000000 INFO @ Tue, 14 Jul 2020 10:42:46: 6000000 INFO @ Tue, 14 Jul 2020 10:42:54: 3000000 INFO @ Tue, 14 Jul 2020 10:42:55: 7000000 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 10:42:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8347277/SRX8347277.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8347277/SRX8347277.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8347277/SRX8347277.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8347277/SRX8347277.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 10:42:57: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:42:57: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:43:03: 8000000 INFO @ Tue, 14 Jul 2020 10:43:04: 4000000 INFO @ Tue, 14 Jul 2020 10:43:07: 1000000 INFO @ Tue, 14 Jul 2020 10:43:12: 9000000 INFO @ Tue, 14 Jul 2020 10:43:13: 5000000 INFO @ Tue, 14 Jul 2020 10:43:18: 2000000 INFO @ Tue, 14 Jul 2020 10:43:21: 10000000 INFO @ Tue, 14 Jul 2020 10:43:22: 6000000 INFO @ Tue, 14 Jul 2020 10:43:28: 3000000 INFO @ Tue, 14 Jul 2020 10:43:29: #1 tag size is determined as 151 bps INFO @ Tue, 14 Jul 2020 10:43:29: #1 tag size = 151 INFO @ Tue, 14 Jul 2020 10:43:29: #1 total tags in treatment: 4512180 INFO @ Tue, 14 Jul 2020 10:43:29: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:43:29: #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 10:43:29: #1 tags after filtering in treatment: 4319558 INFO @ Tue, 14 Jul 2020 10:43:29: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 14 Jul 2020 10:43:29: #1 finished! INFO @ Tue, 14 Jul 2020 10:43:29: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:43:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:43:29: #2 number of paired peaks: 2152 INFO @ Tue, 14 Jul 2020 10:43:29: start model_add_line... INFO @ Tue, 14 Jul 2020 10:43:29: start X-correlation... INFO @ Tue, 14 Jul 2020 10:43:29: end of X-cor INFO @ Tue, 14 Jul 2020 10:43:29: #2 finished! INFO @ Tue, 14 Jul 2020 10:43:29: #2 predicted fragment length is 240 bps INFO @ Tue, 14 Jul 2020 10:43:29: #2 alternative fragment length(s) may be 240 bps INFO @ Tue, 14 Jul 2020 10:43:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8347277/SRX8347277.05_model.r WARNING @ Tue, 14 Jul 2020 10:43:29: #2 Since the d (240) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:43:29: #2 You may need to consider one of the other alternative d(s): 240 WARNING @ Tue, 14 Jul 2020 10:43:29: #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 10:43:29: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:43:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:43:30: 7000000 INFO @ Tue, 14 Jul 2020 10:43:38: 4000000 INFO @ Tue, 14 Jul 2020 10:43:39: 8000000 INFO @ Tue, 14 Jul 2020 10:43:40: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:43:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8347277/SRX8347277.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:43:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8347277/SRX8347277.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:43:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8347277/SRX8347277.05_summits.bed INFO @ Tue, 14 Jul 2020 10:43:46: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5855 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:43:48: 5000000 INFO @ Tue, 14 Jul 2020 10:43:48: 9000000 INFO @ Tue, 14 Jul 2020 10:43:57: 10000000 INFO @ Tue, 14 Jul 2020 10:43:58: 6000000 INFO @ Tue, 14 Jul 2020 10:44:04: #1 tag size is determined as 151 bps INFO @ Tue, 14 Jul 2020 10:44:04: #1 tag size = 151 INFO @ Tue, 14 Jul 2020 10:44:04: #1 total tags in treatment: 4512180 INFO @ Tue, 14 Jul 2020 10:44:04: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:44:04: #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 10:44:04: #1 tags after filtering in treatment: 4319558 INFO @ Tue, 14 Jul 2020 10:44:04: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 14 Jul 2020 10:44:04: #1 finished! INFO @ Tue, 14 Jul 2020 10:44:04: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:44:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:44:05: #2 number of paired peaks: 2152 INFO @ Tue, 14 Jul 2020 10:44:05: start model_add_line... INFO @ Tue, 14 Jul 2020 10:44:05: start X-correlation... INFO @ Tue, 14 Jul 2020 10:44:05: end of X-cor INFO @ Tue, 14 Jul 2020 10:44:05: #2 finished! INFO @ Tue, 14 Jul 2020 10:44:05: #2 predicted fragment length is 240 bps INFO @ Tue, 14 Jul 2020 10:44:05: #2 alternative fragment length(s) may be 240 bps INFO @ Tue, 14 Jul 2020 10:44:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8347277/SRX8347277.10_model.r WARNING @ Tue, 14 Jul 2020 10:44:05: #2 Since the d (240) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:44:05: #2 You may need to consider one of the other alternative d(s): 240 WARNING @ Tue, 14 Jul 2020 10:44:05: #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 10:44:05: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:44:05: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:44:10: 7000000 INFO @ Tue, 14 Jul 2020 10:44:15: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:44:19: 8000000 INFO @ Tue, 14 Jul 2020 10:44:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8347277/SRX8347277.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:44:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8347277/SRX8347277.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:44:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8347277/SRX8347277.10_summits.bed INFO @ Tue, 14 Jul 2020 10:44:20: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3647 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:44:28: 9000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:44:37: 10000000 INFO @ Tue, 14 Jul 2020 10:44:44: #1 tag size is determined as 151 bps INFO @ Tue, 14 Jul 2020 10:44:44: #1 tag size = 151 INFO @ Tue, 14 Jul 2020 10:44:44: #1 total tags in treatment: 4512180 INFO @ Tue, 14 Jul 2020 10:44:44: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:44:44: #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 10:44:44: #1 tags after filtering in treatment: 4319558 INFO @ Tue, 14 Jul 2020 10:44:44: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 14 Jul 2020 10:44:44: #1 finished! INFO @ Tue, 14 Jul 2020 10:44:44: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:44:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:44:44: #2 number of paired peaks: 2152 INFO @ Tue, 14 Jul 2020 10:44:44: start model_add_line... INFO @ Tue, 14 Jul 2020 10:44:44: start X-correlation... INFO @ Tue, 14 Jul 2020 10:44:44: end of X-cor INFO @ Tue, 14 Jul 2020 10:44:44: #2 finished! INFO @ Tue, 14 Jul 2020 10:44:44: #2 predicted fragment length is 240 bps INFO @ Tue, 14 Jul 2020 10:44:44: #2 alternative fragment length(s) may be 240 bps INFO @ Tue, 14 Jul 2020 10:44:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8347277/SRX8347277.20_model.r WARNING @ Tue, 14 Jul 2020 10:44:44: #2 Since the d (240) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:44:44: #2 You may need to consider one of the other alternative d(s): 240 WARNING @ Tue, 14 Jul 2020 10:44:44: #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 10:44:44: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:44:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:44:54: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:44:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8347277/SRX8347277.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:44:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8347277/SRX8347277.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:44:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8347277/SRX8347277.20_summits.bed INFO @ Tue, 14 Jul 2020 10:44:59: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1882 records, 4 fields): 4 millis CompletedMACS2peakCalling