Job ID = 6626976 SRX = SRX7974996 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-14T00:07:21 prefetch.2.10.7: 1) Downloading 'SRR11396283'... 2020-07-14T00:07:21 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T00:31:35 prefetch.2.10.7: HTTPS download failed 2020-07-14T00:31:35 prefetch.2.10.7: 1) failed to download SRR11396283 2020-07-14T00:31:47 prefetch.2.10.7: 1) Downloading 'SRR11396283'... 2020-07-14T00:31:47 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T00:31:47 prefetch.2.10.7: Continue download of 'SRR11396283' from 3239423187 2020-07-14T00:31:52 prefetch.2.10.7: HTTPS download succeed 2020-07-14T00:31:52 prefetch.2.10.7: 1) 'SRR11396283' was downloaded successfully 2020-07-14T00:31:52 prefetch.2.10.7: 'SRR11396283' has 0 unresolved dependencies Read 37186811 spots for SRR11396283/SRR11396283.sra Written 37186811 spots for SRR11396283/SRR11396283.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627467 ("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: 01:19:59 37186811 reads; of these: 37186811 (100.00%) were paired; of these: 18413901 (49.52%) aligned concordantly 0 times 14210043 (38.21%) aligned concordantly exactly 1 time 4562867 (12.27%) aligned concordantly >1 times ---- 18413901 pairs aligned concordantly 0 times; of these: 1961598 (10.65%) aligned discordantly 1 time ---- 16452303 pairs aligned 0 times concordantly or discordantly; of these: 32904606 mates make up the pairs; of these: 28995100 (88.12%) aligned 0 times 1860215 (5.65%) aligned exactly 1 time 2049291 (6.23%) aligned >1 times 61.01% overall alignment rate Time searching: 01:19:59 Overall time: 01:19:59 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] 11954760 / 20691682 = 0.5778 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 11:08:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7974996/SRX7974996.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7974996/SRX7974996.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7974996/SRX7974996.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7974996/SRX7974996.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 11:08:14: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:08:14: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:08:20: 1000000 INFO @ Tue, 14 Jul 2020 11:08:25: 2000000 INFO @ Tue, 14 Jul 2020 11:08:31: 3000000 INFO @ Tue, 14 Jul 2020 11:08:36: 4000000 INFO @ Tue, 14 Jul 2020 11:08:42: 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, 14 Jul 2020 11:08:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7974996/SRX7974996.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7974996/SRX7974996.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7974996/SRX7974996.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7974996/SRX7974996.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 11:08:44: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:08:44: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:08:47: 6000000 INFO @ Tue, 14 Jul 2020 11:08:50: 1000000 INFO @ Tue, 14 Jul 2020 11:08:53: 7000000 INFO @ Tue, 14 Jul 2020 11:08:56: 2000000 INFO @ Tue, 14 Jul 2020 11:08:59: 8000000 INFO @ Tue, 14 Jul 2020 11:09:02: 3000000 INFO @ Tue, 14 Jul 2020 11:09:05: 9000000 INFO @ Tue, 14 Jul 2020 11:09:07: 4000000 INFO @ Tue, 14 Jul 2020 11:09:10: 10000000 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 11:09:13: 5000000 INFO @ Tue, 14 Jul 2020 11:09:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7974996/SRX7974996.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7974996/SRX7974996.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7974996/SRX7974996.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7974996/SRX7974996.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 11:09:14: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:09:14: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:09:16: 11000000 INFO @ Tue, 14 Jul 2020 11:09:19: 6000000 INFO @ Tue, 14 Jul 2020 11:09:21: 1000000 INFO @ Tue, 14 Jul 2020 11:09:22: 12000000 INFO @ Tue, 14 Jul 2020 11:09:25: 7000000 INFO @ Tue, 14 Jul 2020 11:09:27: 2000000 INFO @ Tue, 14 Jul 2020 11:09:28: 13000000 INFO @ Tue, 14 Jul 2020 11:09:31: 8000000 INFO @ Tue, 14 Jul 2020 11:09:33: 3000000 INFO @ Tue, 14 Jul 2020 11:09:33: 14000000 INFO @ Tue, 14 Jul 2020 11:09:37: 9000000 INFO @ Tue, 14 Jul 2020 11:09:38: 4000000 INFO @ Tue, 14 Jul 2020 11:09:39: 15000000 INFO @ Tue, 14 Jul 2020 11:09:43: 10000000 INFO @ Tue, 14 Jul 2020 11:09:44: 5000000 INFO @ Tue, 14 Jul 2020 11:09:45: 16000000 INFO @ Tue, 14 Jul 2020 11:09:49: 11000000 INFO @ Tue, 14 Jul 2020 11:09:50: 6000000 INFO @ Tue, 14 Jul 2020 11:09:51: 17000000 INFO @ Tue, 14 Jul 2020 11:09:54: 12000000 INFO @ Tue, 14 Jul 2020 11:09:56: 7000000 INFO @ Tue, 14 Jul 2020 11:09:57: 18000000 INFO @ Tue, 14 Jul 2020 11:10:00: 13000000 INFO @ Tue, 14 Jul 2020 11:10:02: 8000000 INFO @ Tue, 14 Jul 2020 11:10:03: 19000000 INFO @ Tue, 14 Jul 2020 11:10:06: 14000000 INFO @ Tue, 14 Jul 2020 11:10:08: 9000000 INFO @ Tue, 14 Jul 2020 11:10:09: 20000000 INFO @ Tue, 14 Jul 2020 11:10:12: 15000000 INFO @ Tue, 14 Jul 2020 11:10:13: 10000000 INFO @ Tue, 14 Jul 2020 11:10:15: 21000000 INFO @ Tue, 14 Jul 2020 11:10:18: 16000000 INFO @ Tue, 14 Jul 2020 11:10:18: #1 tag size is determined as 100 bps INFO @ Tue, 14 Jul 2020 11:10:18: #1 tag size = 100 INFO @ Tue, 14 Jul 2020 11:10:18: #1 total tags in treatment: 7754576 INFO @ Tue, 14 Jul 2020 11:10:18: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:10:18: #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 11:10:18: #1 tags after filtering in treatment: 7036936 INFO @ Tue, 14 Jul 2020 11:10:18: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 14 Jul 2020 11:10:18: #1 finished! INFO @ Tue, 14 Jul 2020 11:10:18: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:10:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:10:19: #2 number of paired peaks: 622 WARNING @ Tue, 14 Jul 2020 11:10:19: Fewer paired peaks (622) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 622 pairs to build model! INFO @ Tue, 14 Jul 2020 11:10:19: start model_add_line... INFO @ Tue, 14 Jul 2020 11:10:19: start X-correlation... INFO @ Tue, 14 Jul 2020 11:10:19: end of X-cor INFO @ Tue, 14 Jul 2020 11:10:19: #2 finished! INFO @ Tue, 14 Jul 2020 11:10:19: #2 predicted fragment length is 139 bps INFO @ Tue, 14 Jul 2020 11:10:19: #2 alternative fragment length(s) may be 139 bps INFO @ Tue, 14 Jul 2020 11:10:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7974996/SRX7974996.05_model.r WARNING @ Tue, 14 Jul 2020 11:10:19: #2 Since the d (139) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:10:19: #2 You may need to consider one of the other alternative d(s): 139 WARNING @ Tue, 14 Jul 2020 11:10:19: #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 11:10:19: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:10:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:10:19: 11000000 INFO @ Tue, 14 Jul 2020 11:10:24: 17000000 INFO @ Tue, 14 Jul 2020 11:10:25: 12000000 INFO @ Tue, 14 Jul 2020 11:10:30: 18000000 INFO @ Tue, 14 Jul 2020 11:10:31: 13000000 INFO @ Tue, 14 Jul 2020 11:10:33: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:10:36: 19000000 INFO @ Tue, 14 Jul 2020 11:10:36: 14000000 INFO @ Tue, 14 Jul 2020 11:10:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7974996/SRX7974996.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:10:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7974996/SRX7974996.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:10:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7974996/SRX7974996.05_summits.bed INFO @ Tue, 14 Jul 2020 11:10:40: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (3476 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:10:42: 20000000 INFO @ Tue, 14 Jul 2020 11:10:42: 15000000 INFO @ Tue, 14 Jul 2020 11:10:48: 21000000 INFO @ Tue, 14 Jul 2020 11:10:48: 16000000 INFO @ Tue, 14 Jul 2020 11:10:50: #1 tag size is determined as 100 bps INFO @ Tue, 14 Jul 2020 11:10:50: #1 tag size = 100 INFO @ Tue, 14 Jul 2020 11:10:50: #1 total tags in treatment: 7754576 INFO @ Tue, 14 Jul 2020 11:10:50: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:10:50: #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 11:10:51: #1 tags after filtering in treatment: 7036936 INFO @ Tue, 14 Jul 2020 11:10:51: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 14 Jul 2020 11:10:51: #1 finished! INFO @ Tue, 14 Jul 2020 11:10:51: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:10:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:10:51: #2 number of paired peaks: 622 WARNING @ Tue, 14 Jul 2020 11:10:51: Fewer paired peaks (622) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 622 pairs to build model! INFO @ Tue, 14 Jul 2020 11:10:51: start model_add_line... INFO @ Tue, 14 Jul 2020 11:10:51: start X-correlation... INFO @ Tue, 14 Jul 2020 11:10:51: end of X-cor INFO @ Tue, 14 Jul 2020 11:10:51: #2 finished! INFO @ Tue, 14 Jul 2020 11:10:51: #2 predicted fragment length is 139 bps INFO @ Tue, 14 Jul 2020 11:10:51: #2 alternative fragment length(s) may be 139 bps INFO @ Tue, 14 Jul 2020 11:10:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7974996/SRX7974996.10_model.r WARNING @ Tue, 14 Jul 2020 11:10:51: #2 Since the d (139) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:10:51: #2 You may need to consider one of the other alternative d(s): 139 WARNING @ Tue, 14 Jul 2020 11:10:51: #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 11:10:51: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:10:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:10:54: 17000000 INFO @ Tue, 14 Jul 2020 11:11:00: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:11:06: 19000000 INFO @ Tue, 14 Jul 2020 11:11:06: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:11:12: 20000000 INFO @ Tue, 14 Jul 2020 11:11:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7974996/SRX7974996.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:11:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7974996/SRX7974996.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:11:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7974996/SRX7974996.10_summits.bed INFO @ Tue, 14 Jul 2020 11:11:14: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1766 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:11:17: 21000000 INFO @ Tue, 14 Jul 2020 11:11:20: #1 tag size is determined as 100 bps INFO @ Tue, 14 Jul 2020 11:11:20: #1 tag size = 100 INFO @ Tue, 14 Jul 2020 11:11:20: #1 total tags in treatment: 7754576 INFO @ Tue, 14 Jul 2020 11:11:20: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:11:20: #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 11:11:20: #1 tags after filtering in treatment: 7036936 INFO @ Tue, 14 Jul 2020 11:11:20: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 14 Jul 2020 11:11:20: #1 finished! INFO @ Tue, 14 Jul 2020 11:11:20: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:11:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:11:21: #2 number of paired peaks: 622 WARNING @ Tue, 14 Jul 2020 11:11:21: Fewer paired peaks (622) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 622 pairs to build model! INFO @ Tue, 14 Jul 2020 11:11:21: start model_add_line... INFO @ Tue, 14 Jul 2020 11:11:21: start X-correlation... INFO @ Tue, 14 Jul 2020 11:11:21: end of X-cor INFO @ Tue, 14 Jul 2020 11:11:21: #2 finished! INFO @ Tue, 14 Jul 2020 11:11:21: #2 predicted fragment length is 139 bps INFO @ Tue, 14 Jul 2020 11:11:21: #2 alternative fragment length(s) may be 139 bps INFO @ Tue, 14 Jul 2020 11:11:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7974996/SRX7974996.20_model.r WARNING @ Tue, 14 Jul 2020 11:11:21: #2 Since the d (139) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:11:21: #2 You may need to consider one of the other alternative d(s): 139 WARNING @ Tue, 14 Jul 2020 11:11:21: #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 11:11:21: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:11:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:11:36: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:11:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7974996/SRX7974996.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:11:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7974996/SRX7974996.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:11:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7974996/SRX7974996.20_summits.bed INFO @ Tue, 14 Jul 2020 11:11:44: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (802 records, 4 fields): 11 millis CompletedMACS2peakCalling