Job ID = 6626975 SRX = SRX7974995 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 'SRR11396284'... 2020-07-14T00:07:21 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T00:12:26 prefetch.2.10.7: HTTPS download succeed 2020-07-14T00:12:26 prefetch.2.10.7: 1) 'SRR11396284' was downloaded successfully Read 13046005 spots for SRR11396284/SRR11396284.sra Written 13046005 spots for SRR11396284/SRR11396284.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627250 ("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: 00:27:54 13046005 reads; of these: 13046005 (100.00%) were paired; of these: 4296838 (32.94%) aligned concordantly 0 times 6274251 (48.09%) aligned concordantly exactly 1 time 2474916 (18.97%) aligned concordantly >1 times ---- 4296838 pairs aligned concordantly 0 times; of these: 56314 (1.31%) aligned discordantly 1 time ---- 4240524 pairs aligned 0 times concordantly or discordantly; of these: 8481048 mates make up the pairs; of these: 8107431 (95.59%) aligned 0 times 220544 (2.60%) aligned exactly 1 time 153073 (1.80%) aligned >1 times 68.93% overall alignment rate Time searching: 00:27:54 Overall time: 00:27:54 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 8 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] 1646320 / 8789848 = 0.1873 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 09:50:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7974995/SRX7974995.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7974995/SRX7974995.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7974995/SRX7974995.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7974995/SRX7974995.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 09:50:29: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:50:29: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:50:36: 1000000 INFO @ Tue, 14 Jul 2020 09:50:42: 2000000 INFO @ Tue, 14 Jul 2020 09:50:49: 3000000 INFO @ Tue, 14 Jul 2020 09:50:56: 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 09:50:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7974995/SRX7974995.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7974995/SRX7974995.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7974995/SRX7974995.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7974995/SRX7974995.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 09:50:59: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:50:59: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:51:04: 5000000 INFO @ Tue, 14 Jul 2020 09:51:06: 1000000 INFO @ Tue, 14 Jul 2020 09:51:13: 2000000 INFO @ Tue, 14 Jul 2020 09:51:13: 6000000 INFO @ Tue, 14 Jul 2020 09:51:19: 3000000 INFO @ Tue, 14 Jul 2020 09:51:22: 7000000 INFO @ Tue, 14 Jul 2020 09:51:26: 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 09:51:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7974995/SRX7974995.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7974995/SRX7974995.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7974995/SRX7974995.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7974995/SRX7974995.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 09:51:29: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:51:29: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:51:30: 8000000 INFO @ Tue, 14 Jul 2020 09:51:33: 5000000 INFO @ Tue, 14 Jul 2020 09:51:36: 1000000 INFO @ Tue, 14 Jul 2020 09:51:39: 9000000 INFO @ Tue, 14 Jul 2020 09:51:40: 6000000 INFO @ Tue, 14 Jul 2020 09:51:43: 2000000 INFO @ Tue, 14 Jul 2020 09:51:46: 7000000 INFO @ Tue, 14 Jul 2020 09:51:48: 10000000 INFO @ Tue, 14 Jul 2020 09:51:50: 3000000 INFO @ Tue, 14 Jul 2020 09:51:53: 8000000 INFO @ Tue, 14 Jul 2020 09:51:57: 4000000 INFO @ Tue, 14 Jul 2020 09:51:57: 11000000 INFO @ Tue, 14 Jul 2020 09:52:00: 9000000 INFO @ Tue, 14 Jul 2020 09:52:03: 5000000 INFO @ Tue, 14 Jul 2020 09:52:06: 12000000 INFO @ Tue, 14 Jul 2020 09:52:07: 10000000 INFO @ Tue, 14 Jul 2020 09:52:10: 6000000 INFO @ Tue, 14 Jul 2020 09:52:14: 11000000 INFO @ Tue, 14 Jul 2020 09:52:16: 13000000 INFO @ Tue, 14 Jul 2020 09:52:17: 7000000 INFO @ Tue, 14 Jul 2020 09:52:21: 12000000 INFO @ Tue, 14 Jul 2020 09:52:24: 8000000 INFO @ Tue, 14 Jul 2020 09:52:26: 14000000 INFO @ Tue, 14 Jul 2020 09:52:28: 13000000 INFO @ Tue, 14 Jul 2020 09:52:31: 9000000 INFO @ Tue, 14 Jul 2020 09:52:32: #1 tag size is determined as 100 bps INFO @ Tue, 14 Jul 2020 09:52:32: #1 tag size = 100 INFO @ Tue, 14 Jul 2020 09:52:32: #1 total tags in treatment: 7107808 INFO @ Tue, 14 Jul 2020 09:52:32: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:52:32: #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 09:52:32: #1 tags after filtering in treatment: 6733195 INFO @ Tue, 14 Jul 2020 09:52:32: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 14 Jul 2020 09:52:32: #1 finished! INFO @ Tue, 14 Jul 2020 09:52:32: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:52:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:52:33: #2 number of paired peaks: 274 WARNING @ Tue, 14 Jul 2020 09:52:33: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Tue, 14 Jul 2020 09:52:33: start model_add_line... INFO @ Tue, 14 Jul 2020 09:52:33: start X-correlation... INFO @ Tue, 14 Jul 2020 09:52:33: end of X-cor INFO @ Tue, 14 Jul 2020 09:52:33: #2 finished! INFO @ Tue, 14 Jul 2020 09:52:33: #2 predicted fragment length is 133 bps INFO @ Tue, 14 Jul 2020 09:52:33: #2 alternative fragment length(s) may be 133 bps INFO @ Tue, 14 Jul 2020 09:52:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7974995/SRX7974995.05_model.r WARNING @ Tue, 14 Jul 2020 09:52:33: #2 Since the d (133) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:52:33: #2 You may need to consider one of the other alternative d(s): 133 WARNING @ Tue, 14 Jul 2020 09:52:33: #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 09:52:33: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:52:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:52:35: 14000000 INFO @ Tue, 14 Jul 2020 09:52:38: 10000000 INFO @ Tue, 14 Jul 2020 09:52:40: #1 tag size is determined as 100 bps INFO @ Tue, 14 Jul 2020 09:52:40: #1 tag size = 100 INFO @ Tue, 14 Jul 2020 09:52:40: #1 total tags in treatment: 7107808 INFO @ Tue, 14 Jul 2020 09:52:40: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:52:40: #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 09:52:40: #1 tags after filtering in treatment: 6733195 INFO @ Tue, 14 Jul 2020 09:52:40: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 14 Jul 2020 09:52:40: #1 finished! INFO @ Tue, 14 Jul 2020 09:52:40: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:52:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:52:41: #2 number of paired peaks: 274 WARNING @ Tue, 14 Jul 2020 09:52:41: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Tue, 14 Jul 2020 09:52:41: start model_add_line... INFO @ Tue, 14 Jul 2020 09:52:41: start X-correlation... INFO @ Tue, 14 Jul 2020 09:52:41: end of X-cor INFO @ Tue, 14 Jul 2020 09:52:41: #2 finished! INFO @ Tue, 14 Jul 2020 09:52:41: #2 predicted fragment length is 133 bps INFO @ Tue, 14 Jul 2020 09:52:41: #2 alternative fragment length(s) may be 133 bps INFO @ Tue, 14 Jul 2020 09:52:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7974995/SRX7974995.10_model.r WARNING @ Tue, 14 Jul 2020 09:52:41: #2 Since the d (133) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:52:41: #2 You may need to consider one of the other alternative d(s): 133 WARNING @ Tue, 14 Jul 2020 09:52:41: #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 09:52:41: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:52:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:52:45: 11000000 INFO @ Tue, 14 Jul 2020 09:52:49: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:52:52: 12000000 INFO @ Tue, 14 Jul 2020 09:52:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7974995/SRX7974995.05_peaks.xls INFO @ Tue, 14 Jul 2020 09:52:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7974995/SRX7974995.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:52:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7974995/SRX7974995.05_summits.bed INFO @ Tue, 14 Jul 2020 09:52:58: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1764 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:52:58: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:52:59: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 09:53:06: 14000000 INFO @ Tue, 14 Jul 2020 09:53:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7974995/SRX7974995.10_peaks.xls INFO @ Tue, 14 Jul 2020 09:53:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7974995/SRX7974995.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:53:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7974995/SRX7974995.10_summits.bed INFO @ Tue, 14 Jul 2020 09:53:07: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (720 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:53:11: #1 tag size is determined as 100 bps INFO @ Tue, 14 Jul 2020 09:53:11: #1 tag size = 100 INFO @ Tue, 14 Jul 2020 09:53:11: #1 total tags in treatment: 7107808 INFO @ Tue, 14 Jul 2020 09:53:11: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:53:11: #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 09:53:11: #1 tags after filtering in treatment: 6733195 INFO @ Tue, 14 Jul 2020 09:53:11: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 14 Jul 2020 09:53:11: #1 finished! INFO @ Tue, 14 Jul 2020 09:53:11: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:53:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:53:11: #2 number of paired peaks: 274 WARNING @ Tue, 14 Jul 2020 09:53:11: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Tue, 14 Jul 2020 09:53:11: start model_add_line... INFO @ Tue, 14 Jul 2020 09:53:11: start X-correlation... INFO @ Tue, 14 Jul 2020 09:53:11: end of X-cor INFO @ Tue, 14 Jul 2020 09:53:11: #2 finished! INFO @ Tue, 14 Jul 2020 09:53:11: #2 predicted fragment length is 133 bps INFO @ Tue, 14 Jul 2020 09:53:11: #2 alternative fragment length(s) may be 133 bps INFO @ Tue, 14 Jul 2020 09:53:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7974995/SRX7974995.20_model.r WARNING @ Tue, 14 Jul 2020 09:53:11: #2 Since the d (133) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:53:11: #2 You may need to consider one of the other alternative d(s): 133 WARNING @ Tue, 14 Jul 2020 09:53:11: #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 09:53:11: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:53:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:53:27: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 09:53:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7974995/SRX7974995.20_peaks.xls INFO @ Tue, 14 Jul 2020 09:53:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7974995/SRX7974995.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:53:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7974995/SRX7974995.20_summits.bed INFO @ Tue, 14 Jul 2020 09:53:35: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (400 records, 4 fields): 2 millis CompletedMACS2peakCalling