Job ID = 6627075 SRX = SRX8347284 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-14T00:45:32 prefetch.2.10.7: 1) Downloading 'SRR11795467'... 2020-07-14T00:45:32 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T00:54:19 prefetch.2.10.7: HTTPS download succeed 2020-07-14T00:54:19 prefetch.2.10.7: 1) 'SRR11795467' was downloaded successfully 2020-07-14T00:54:19 prefetch.2.10.7: 'SRR11795467' has 0 unresolved dependencies Read 15407373 spots for SRR11795467/SRR11795467.sra Written 15407373 spots for SRR11795467/SRR11795467.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627409 ("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: 00:39:30 15407373 reads; of these: 15407373 (100.00%) were paired; of these: 3655480 (23.73%) aligned concordantly 0 times 9595504 (62.28%) aligned concordantly exactly 1 time 2156389 (14.00%) aligned concordantly >1 times ---- 3655480 pairs aligned concordantly 0 times; of these: 874738 (23.93%) aligned discordantly 1 time ---- 2780742 pairs aligned 0 times concordantly or discordantly; of these: 5561484 mates make up the pairs; of these: 4825701 (86.77%) aligned 0 times 287720 (5.17%) aligned exactly 1 time 448063 (8.06%) aligned >1 times 84.34% overall alignment rate Time searching: 00:39:30 Overall time: 00:39:30 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] 4466112 / 12579544 = 0.3550 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 10:45:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8347284/SRX8347284.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8347284/SRX8347284.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8347284/SRX8347284.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8347284/SRX8347284.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 10:45:47: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:45:47: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:45:55: 1000000 INFO @ Tue, 14 Jul 2020 10:46:04: 2000000 INFO @ Tue, 14 Jul 2020 10:46:13: 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 10:46:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8347284/SRX8347284.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8347284/SRX8347284.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8347284/SRX8347284.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8347284/SRX8347284.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 10:46:16: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:46:16: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:46:21: 4000000 INFO @ Tue, 14 Jul 2020 10:46:23: 1000000 INFO @ Tue, 14 Jul 2020 10:46:30: 5000000 INFO @ Tue, 14 Jul 2020 10:46:30: 2000000 INFO @ Tue, 14 Jul 2020 10:46:37: 3000000 INFO @ Tue, 14 Jul 2020 10:46:39: 6000000 INFO @ Tue, 14 Jul 2020 10:46:44: 4000000 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 10:46:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8347284/SRX8347284.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8347284/SRX8347284.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8347284/SRX8347284.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8347284/SRX8347284.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 10:46:46: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:46:46: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:46:48: 7000000 INFO @ Tue, 14 Jul 2020 10:46:51: 5000000 INFO @ Tue, 14 Jul 2020 10:46:55: 1000000 INFO @ Tue, 14 Jul 2020 10:46:57: 8000000 INFO @ Tue, 14 Jul 2020 10:46:57: 6000000 INFO @ Tue, 14 Jul 2020 10:47:04: 2000000 INFO @ Tue, 14 Jul 2020 10:47:04: 7000000 INFO @ Tue, 14 Jul 2020 10:47:05: 9000000 INFO @ Tue, 14 Jul 2020 10:47:11: 8000000 INFO @ Tue, 14 Jul 2020 10:47:13: 3000000 INFO @ Tue, 14 Jul 2020 10:47:13: 10000000 INFO @ Tue, 14 Jul 2020 10:47:17: 9000000 INFO @ Tue, 14 Jul 2020 10:47:21: 4000000 INFO @ Tue, 14 Jul 2020 10:47:22: 11000000 INFO @ Tue, 14 Jul 2020 10:47:25: 10000000 INFO @ Tue, 14 Jul 2020 10:47:30: 5000000 INFO @ Tue, 14 Jul 2020 10:47:31: 12000000 INFO @ Tue, 14 Jul 2020 10:47:37: 11000000 INFO @ Tue, 14 Jul 2020 10:47:39: 6000000 INFO @ Tue, 14 Jul 2020 10:47:40: 13000000 INFO @ Tue, 14 Jul 2020 10:47:44: 12000000 INFO @ Tue, 14 Jul 2020 10:47:48: 7000000 INFO @ Tue, 14 Jul 2020 10:47:48: 14000000 INFO @ Tue, 14 Jul 2020 10:47:51: 13000000 INFO @ Tue, 14 Jul 2020 10:47:56: 8000000 INFO @ Tue, 14 Jul 2020 10:47:57: 15000000 INFO @ Tue, 14 Jul 2020 10:47:58: 14000000 INFO @ Tue, 14 Jul 2020 10:48:04: 9000000 INFO @ Tue, 14 Jul 2020 10:48:05: 15000000 INFO @ Tue, 14 Jul 2020 10:48:05: 16000000 INFO @ Tue, 14 Jul 2020 10:48:11: 16000000 INFO @ Tue, 14 Jul 2020 10:48:12: 10000000 INFO @ Tue, 14 Jul 2020 10:48:14: 17000000 INFO @ Tue, 14 Jul 2020 10:48:14: #1 tag size is determined as 150 bps INFO @ Tue, 14 Jul 2020 10:48:14: #1 tag size = 150 INFO @ Tue, 14 Jul 2020 10:48:14: #1 total tags in treatment: 7474678 INFO @ Tue, 14 Jul 2020 10:48:14: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:48:14: #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 10:48:14: #1 tags after filtering in treatment: 7273780 INFO @ Tue, 14 Jul 2020 10:48:14: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 14 Jul 2020 10:48:14: #1 finished! INFO @ Tue, 14 Jul 2020 10:48:14: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:48:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:48:15: #2 number of paired peaks: 103 WARNING @ Tue, 14 Jul 2020 10:48:15: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Tue, 14 Jul 2020 10:48:15: start model_add_line... INFO @ Tue, 14 Jul 2020 10:48:15: start X-correlation... INFO @ Tue, 14 Jul 2020 10:48:15: end of X-cor INFO @ Tue, 14 Jul 2020 10:48:15: #2 finished! INFO @ Tue, 14 Jul 2020 10:48:15: #2 predicted fragment length is 193 bps INFO @ Tue, 14 Jul 2020 10:48:15: #2 alternative fragment length(s) may be 193 bps INFO @ Tue, 14 Jul 2020 10:48:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8347284/SRX8347284.05_model.r WARNING @ Tue, 14 Jul 2020 10:48:15: #2 Since the d (193) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:48:15: #2 You may need to consider one of the other alternative d(s): 193 WARNING @ Tue, 14 Jul 2020 10:48:15: #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 10:48:15: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:48:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:48:18: 17000000 INFO @ Tue, 14 Jul 2020 10:48:18: #1 tag size is determined as 150 bps INFO @ Tue, 14 Jul 2020 10:48:18: #1 tag size = 150 INFO @ Tue, 14 Jul 2020 10:48:18: #1 total tags in treatment: 7474678 INFO @ Tue, 14 Jul 2020 10:48:18: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:48:18: #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 10:48:19: #1 tags after filtering in treatment: 7273780 INFO @ Tue, 14 Jul 2020 10:48:19: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 14 Jul 2020 10:48:19: #1 finished! INFO @ Tue, 14 Jul 2020 10:48:19: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:48:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:48:19: #2 number of paired peaks: 103 WARNING @ Tue, 14 Jul 2020 10:48:19: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Tue, 14 Jul 2020 10:48:19: start model_add_line... INFO @ Tue, 14 Jul 2020 10:48:19: start X-correlation... INFO @ Tue, 14 Jul 2020 10:48:19: end of X-cor INFO @ Tue, 14 Jul 2020 10:48:19: #2 finished! INFO @ Tue, 14 Jul 2020 10:48:19: #2 predicted fragment length is 193 bps INFO @ Tue, 14 Jul 2020 10:48:19: #2 alternative fragment length(s) may be 193 bps INFO @ Tue, 14 Jul 2020 10:48:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8347284/SRX8347284.10_model.r WARNING @ Tue, 14 Jul 2020 10:48:19: #2 Since the d (193) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:48:19: #2 You may need to consider one of the other alternative d(s): 193 WARNING @ Tue, 14 Jul 2020 10:48:19: #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 10:48:19: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:48:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:48:21: 11000000 INFO @ Tue, 14 Jul 2020 10:48:29: 12000000 INFO @ Tue, 14 Jul 2020 10:48:33: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:48:36: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:48:38: 13000000 INFO @ Tue, 14 Jul 2020 10:48:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8347284/SRX8347284.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:48:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8347284/SRX8347284.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:48:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8347284/SRX8347284.05_summits.bed INFO @ Tue, 14 Jul 2020 10:48:42: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (3360 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:48:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8347284/SRX8347284.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:48:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8347284/SRX8347284.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:48:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8347284/SRX8347284.10_summits.bed INFO @ Tue, 14 Jul 2020 10:48:44: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1129 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:48:47: 14000000 INFO @ Tue, 14 Jul 2020 10:48:55: 15000000 INFO @ Tue, 14 Jul 2020 10:49:02: 16000000 INFO @ Tue, 14 Jul 2020 10:49:10: 17000000 INFO @ Tue, 14 Jul 2020 10:49:11: #1 tag size is determined as 150 bps INFO @ Tue, 14 Jul 2020 10:49:11: #1 tag size = 150 INFO @ Tue, 14 Jul 2020 10:49:11: #1 total tags in treatment: 7474678 INFO @ Tue, 14 Jul 2020 10:49:11: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:49:11: #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 10:49:11: #1 tags after filtering in treatment: 7273780 INFO @ Tue, 14 Jul 2020 10:49:11: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 14 Jul 2020 10:49:11: #1 finished! INFO @ Tue, 14 Jul 2020 10:49:11: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:49:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:49:11: #2 number of paired peaks: 103 WARNING @ Tue, 14 Jul 2020 10:49:11: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Tue, 14 Jul 2020 10:49:11: start model_add_line... INFO @ Tue, 14 Jul 2020 10:49:11: start X-correlation... INFO @ Tue, 14 Jul 2020 10:49:11: end of X-cor INFO @ Tue, 14 Jul 2020 10:49:11: #2 finished! INFO @ Tue, 14 Jul 2020 10:49:11: #2 predicted fragment length is 193 bps INFO @ Tue, 14 Jul 2020 10:49:11: #2 alternative fragment length(s) may be 193 bps INFO @ Tue, 14 Jul 2020 10:49:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8347284/SRX8347284.20_model.r WARNING @ Tue, 14 Jul 2020 10:49:11: #2 Since the d (193) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:49:11: #2 You may need to consider one of the other alternative d(s): 193 WARNING @ Tue, 14 Jul 2020 10:49:11: #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 10:49:11: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:49:11: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:49:29: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:49:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8347284/SRX8347284.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:49:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8347284/SRX8347284.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:49:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8347284/SRX8347284.20_summits.bed INFO @ Tue, 14 Jul 2020 10:49:37: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (245 records, 4 fields): 1 millis CompletedMACS2peakCalling