Job ID = 6626974 SRX = SRX7974994 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-14T00:07:06 prefetch.2.10.7: 1) Downloading 'SRR11396285'... 2020-07-14T00:07:06 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T00:21:27 prefetch.2.10.7: HTTPS download failed 2020-07-14T00:21:27 prefetch.2.10.7: 1) failed to download SRR11396285 2020-07-14T00:21:39 prefetch.2.10.7: 1) Downloading 'SRR11396285'... 2020-07-14T00:21:39 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T00:21:39 prefetch.2.10.7: Continue download of 'SRR11396285' from 3168180852 2020-07-14T00:21:43 prefetch.2.10.7: HTTPS download succeed 2020-07-14T00:21:43 prefetch.2.10.7: 1) 'SRR11396285' was downloaded successfully 2020-07-14T00:21:43 prefetch.2.10.7: 'SRR11396285' has 0 unresolved dependencies Read 35532428 spots for SRR11396285/SRR11396285.sra Written 35532428 spots for SRR11396285/SRR11396285.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627423 ("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: 01:15:48 35532428 reads; of these: 35532428 (100.00%) were paired; of these: 16013851 (45.07%) aligned concordantly 0 times 13843640 (38.96%) aligned concordantly exactly 1 time 5674937 (15.97%) aligned concordantly >1 times ---- 16013851 pairs aligned concordantly 0 times; of these: 1304222 (8.14%) aligned discordantly 1 time ---- 14709629 pairs aligned 0 times concordantly or discordantly; of these: 29419258 mates make up the pairs; of these: 26483720 (90.02%) aligned 0 times 1102420 (3.75%) aligned exactly 1 time 1833118 (6.23%) aligned >1 times 62.73% overall alignment rate Time searching: 01:15:48 Overall time: 01:15:48 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] 7957527 / 20802022 = 0.3825 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 10:54:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7974994/SRX7974994.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7974994/SRX7974994.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7974994/SRX7974994.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7974994/SRX7974994.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 10:54:58: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:54:58: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:55:05: 1000000 INFO @ Tue, 14 Jul 2020 10:55:12: 2000000 INFO @ Tue, 14 Jul 2020 10:55:18: 3000000 INFO @ Tue, 14 Jul 2020 10:55:24: 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 10:55:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7974994/SRX7974994.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7974994/SRX7974994.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7974994/SRX7974994.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7974994/SRX7974994.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 10:55:28: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:55:28: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:55:31: 5000000 INFO @ Tue, 14 Jul 2020 10:55:36: 1000000 INFO @ Tue, 14 Jul 2020 10:55:38: 6000000 INFO @ Tue, 14 Jul 2020 10:55:43: 2000000 INFO @ Tue, 14 Jul 2020 10:55:46: 7000000 INFO @ Tue, 14 Jul 2020 10:55:50: 3000000 INFO @ Tue, 14 Jul 2020 10:55:53: 8000000 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 10:55:57: 4000000 INFO @ Tue, 14 Jul 2020 10:55:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7974994/SRX7974994.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7974994/SRX7974994.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7974994/SRX7974994.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7974994/SRX7974994.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 10:55:58: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:55:58: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:56:00: 9000000 INFO @ Tue, 14 Jul 2020 10:56:04: 5000000 INFO @ Tue, 14 Jul 2020 10:56:06: 1000000 INFO @ Tue, 14 Jul 2020 10:56:07: 10000000 INFO @ Tue, 14 Jul 2020 10:56:11: 6000000 INFO @ Tue, 14 Jul 2020 10:56:13: 2000000 INFO @ Tue, 14 Jul 2020 10:56:14: 11000000 INFO @ Tue, 14 Jul 2020 10:56:19: 7000000 INFO @ Tue, 14 Jul 2020 10:56:20: 3000000 INFO @ Tue, 14 Jul 2020 10:56:22: 12000000 INFO @ Tue, 14 Jul 2020 10:56:26: 8000000 INFO @ Tue, 14 Jul 2020 10:56:27: 4000000 INFO @ Tue, 14 Jul 2020 10:56:29: 13000000 INFO @ Tue, 14 Jul 2020 10:56:33: 9000000 INFO @ Tue, 14 Jul 2020 10:56:35: 5000000 INFO @ Tue, 14 Jul 2020 10:56:36: 14000000 INFO @ Tue, 14 Jul 2020 10:56:40: 10000000 INFO @ Tue, 14 Jul 2020 10:56:42: 6000000 INFO @ Tue, 14 Jul 2020 10:56:43: 15000000 INFO @ Tue, 14 Jul 2020 10:56:47: 11000000 INFO @ Tue, 14 Jul 2020 10:56:49: 7000000 INFO @ Tue, 14 Jul 2020 10:56:50: 16000000 INFO @ Tue, 14 Jul 2020 10:56:55: 12000000 INFO @ Tue, 14 Jul 2020 10:56:56: 8000000 INFO @ Tue, 14 Jul 2020 10:56:57: 17000000 INFO @ Tue, 14 Jul 2020 10:57:02: 13000000 INFO @ Tue, 14 Jul 2020 10:57:03: 9000000 INFO @ Tue, 14 Jul 2020 10:57:04: 18000000 INFO @ Tue, 14 Jul 2020 10:57:09: 14000000 INFO @ Tue, 14 Jul 2020 10:57:11: 10000000 INFO @ Tue, 14 Jul 2020 10:57:11: 19000000 INFO @ Tue, 14 Jul 2020 10:57:16: 15000000 INFO @ Tue, 14 Jul 2020 10:57:18: 11000000 INFO @ Tue, 14 Jul 2020 10:57:19: 20000000 INFO @ Tue, 14 Jul 2020 10:57:23: 16000000 INFO @ Tue, 14 Jul 2020 10:57:25: 12000000 INFO @ Tue, 14 Jul 2020 10:57:26: 21000000 INFO @ Tue, 14 Jul 2020 10:57:30: 17000000 INFO @ Tue, 14 Jul 2020 10:57:32: 13000000 INFO @ Tue, 14 Jul 2020 10:57:33: 22000000 INFO @ Tue, 14 Jul 2020 10:57:37: 18000000 INFO @ Tue, 14 Jul 2020 10:57:39: 14000000 INFO @ Tue, 14 Jul 2020 10:57:41: 23000000 INFO @ Tue, 14 Jul 2020 10:57:45: 19000000 INFO @ Tue, 14 Jul 2020 10:57:46: 15000000 INFO @ Tue, 14 Jul 2020 10:57:48: 24000000 INFO @ Tue, 14 Jul 2020 10:57:52: 20000000 INFO @ Tue, 14 Jul 2020 10:57:53: 16000000 INFO @ Tue, 14 Jul 2020 10:57:55: 25000000 INFO @ Tue, 14 Jul 2020 10:58:00: 21000000 INFO @ Tue, 14 Jul 2020 10:58:00: 17000000 INFO @ Tue, 14 Jul 2020 10:58:03: 26000000 INFO @ Tue, 14 Jul 2020 10:58:07: 22000000 INFO @ Tue, 14 Jul 2020 10:58:07: 18000000 INFO @ Tue, 14 Jul 2020 10:58:10: 27000000 INFO @ Tue, 14 Jul 2020 10:58:14: 23000000 INFO @ Tue, 14 Jul 2020 10:58:14: 19000000 INFO @ Tue, 14 Jul 2020 10:58:17: 28000000 INFO @ Tue, 14 Jul 2020 10:58:21: 24000000 INFO @ Tue, 14 Jul 2020 10:58:22: 20000000 INFO @ Tue, 14 Jul 2020 10:58:22: #1 tag size is determined as 100 bps INFO @ Tue, 14 Jul 2020 10:58:22: #1 tag size = 100 INFO @ Tue, 14 Jul 2020 10:58:22: #1 total tags in treatment: 11941994 INFO @ Tue, 14 Jul 2020 10:58:22: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:58:22: #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 10:58:22: #1 tags after filtering in treatment: 11257257 INFO @ Tue, 14 Jul 2020 10:58:22: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 14 Jul 2020 10:58:22: #1 finished! INFO @ Tue, 14 Jul 2020 10:58:22: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:58:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:58:23: #2 number of paired peaks: 217 WARNING @ Tue, 14 Jul 2020 10:58:23: Fewer paired peaks (217) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 217 pairs to build model! INFO @ Tue, 14 Jul 2020 10:58:23: start model_add_line... INFO @ Tue, 14 Jul 2020 10:58:23: start X-correlation... INFO @ Tue, 14 Jul 2020 10:58:23: end of X-cor INFO @ Tue, 14 Jul 2020 10:58:23: #2 finished! INFO @ Tue, 14 Jul 2020 10:58:23: #2 predicted fragment length is 199 bps INFO @ Tue, 14 Jul 2020 10:58:23: #2 alternative fragment length(s) may be 199 bps INFO @ Tue, 14 Jul 2020 10:58:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7974994/SRX7974994.05_model.r WARNING @ Tue, 14 Jul 2020 10:58:23: #2 Since the d (199) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:58:23: #2 You may need to consider one of the other alternative d(s): 199 WARNING @ Tue, 14 Jul 2020 10:58:23: #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 10:58:23: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:58:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:58:29: 25000000 INFO @ Tue, 14 Jul 2020 10:58:29: 21000000 INFO @ Tue, 14 Jul 2020 10:58:36: 26000000 INFO @ Tue, 14 Jul 2020 10:58:36: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:58:43: 23000000 INFO @ Tue, 14 Jul 2020 10:58:43: 27000000 INFO @ Tue, 14 Jul 2020 10:58:45: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:58:51: 24000000 INFO @ Tue, 14 Jul 2020 10:58:51: 28000000 INFO @ Tue, 14 Jul 2020 10:58:56: #1 tag size is determined as 100 bps INFO @ Tue, 14 Jul 2020 10:58:56: #1 tag size = 100 INFO @ Tue, 14 Jul 2020 10:58:56: #1 total tags in treatment: 11941994 INFO @ Tue, 14 Jul 2020 10:58:56: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:58:56: #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 10:58:56: #1 tags after filtering in treatment: 11257257 INFO @ Tue, 14 Jul 2020 10:58:56: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 14 Jul 2020 10:58:56: #1 finished! INFO @ Tue, 14 Jul 2020 10:58:56: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:58:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:58:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7974994/SRX7974994.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:58:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7974994/SRX7974994.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:58:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7974994/SRX7974994.05_summits.bed INFO @ Tue, 14 Jul 2020 10:58:57: Done! INFO @ Tue, 14 Jul 2020 10:58:57: #2 number of paired peaks: 217 WARNING @ Tue, 14 Jul 2020 10:58:57: Fewer paired peaks (217) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 217 pairs to build model! INFO @ Tue, 14 Jul 2020 10:58:57: start model_add_line... pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7654 records, 4 fields): 8 millis INFO @ Tue, 14 Jul 2020 10:58:57: start X-correlation... INFO @ Tue, 14 Jul 2020 10:58:57: end of X-cor INFO @ Tue, 14 Jul 2020 10:58:57: #2 finished! INFO @ Tue, 14 Jul 2020 10:58:57: #2 predicted fragment length is 199 bps INFO @ Tue, 14 Jul 2020 10:58:57: #2 alternative fragment length(s) may be 199 bps INFO @ Tue, 14 Jul 2020 10:58:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7974994/SRX7974994.10_model.r WARNING @ Tue, 14 Jul 2020 10:58:57: #2 Since the d (199) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:58:57: #2 You may need to consider one of the other alternative d(s): 199 WARNING @ Tue, 14 Jul 2020 10:58:57: #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 10:58:57: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:58:57: #3 Pre-compute pvalue-qvalue table... CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:58:58: 25000000 INFO @ Tue, 14 Jul 2020 10:59:05: 26000000 INFO @ Tue, 14 Jul 2020 10:59:12: 27000000 INFO @ Tue, 14 Jul 2020 10:59:19: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:59:19: 28000000 INFO @ Tue, 14 Jul 2020 10:59:24: #1 tag size is determined as 100 bps INFO @ Tue, 14 Jul 2020 10:59:24: #1 tag size = 100 INFO @ Tue, 14 Jul 2020 10:59:24: #1 total tags in treatment: 11941994 INFO @ Tue, 14 Jul 2020 10:59:24: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:59:24: #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 10:59:24: #1 tags after filtering in treatment: 11257257 INFO @ Tue, 14 Jul 2020 10:59:24: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 14 Jul 2020 10:59:24: #1 finished! INFO @ Tue, 14 Jul 2020 10:59:24: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:59:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:59:25: #2 number of paired peaks: 217 WARNING @ Tue, 14 Jul 2020 10:59:25: Fewer paired peaks (217) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 217 pairs to build model! INFO @ Tue, 14 Jul 2020 10:59:25: start model_add_line... INFO @ Tue, 14 Jul 2020 10:59:25: start X-correlation... INFO @ Tue, 14 Jul 2020 10:59:25: end of X-cor INFO @ Tue, 14 Jul 2020 10:59:25: #2 finished! INFO @ Tue, 14 Jul 2020 10:59:25: #2 predicted fragment length is 199 bps INFO @ Tue, 14 Jul 2020 10:59:25: #2 alternative fragment length(s) may be 199 bps INFO @ Tue, 14 Jul 2020 10:59:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7974994/SRX7974994.20_model.r WARNING @ Tue, 14 Jul 2020 10:59:25: #2 Since the d (199) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:59:25: #2 You may need to consider one of the other alternative d(s): 199 WARNING @ Tue, 14 Jul 2020 10:59:25: #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 10:59:25: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:59:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:59:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7974994/SRX7974994.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:59:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7974994/SRX7974994.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:59:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7974994/SRX7974994.10_summits.bed INFO @ Tue, 14 Jul 2020 10:59:31: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4210 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:59:47: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:59:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7974994/SRX7974994.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:59:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7974994/SRX7974994.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:59:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7974994/SRX7974994.20_summits.bed INFO @ Tue, 14 Jul 2020 10:59:59: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1744 records, 4 fields): 4 millis CompletedMACS2peakCalling