Job ID = 5720428 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,677,165 reads read : 23,677,165 reads written : 23,677,165 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289682.sra.cache’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:48 23677165 reads; of these: 23677165 (100.00%) were unpaired; of these: 3687752 (15.58%) aligned 0 times 14647707 (61.86%) aligned exactly 1 time 5341706 (22.56%) aligned >1 times 84.42% overall alignment rate Time searching: 00:06:48 Overall time: 00:06:48 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 12 files... [bam_rmdupse_core] 6351664 / 19989413 = 0.3178 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 @ Thu, 16 Apr 2020 00:37:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592405/SRX2592405.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592405/SRX2592405.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592405/SRX2592405.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592405/SRX2592405.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 @ Thu, 16 Apr 2020 00:37:09: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:37:09: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:37:14: 1000000 INFO @ Thu, 16 Apr 2020 00:37:19: 2000000 INFO @ Thu, 16 Apr 2020 00:37:24: 3000000 INFO @ Thu, 16 Apr 2020 00:37:29: 4000000 INFO @ Thu, 16 Apr 2020 00:37:34: 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 @ Thu, 16 Apr 2020 00:37:39: 6000000 INFO @ Thu, 16 Apr 2020 00:37:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592405/SRX2592405.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592405/SRX2592405.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592405/SRX2592405.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592405/SRX2592405.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 @ Thu, 16 Apr 2020 00:37:39: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:37:39: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:37:44: 7000000 INFO @ Thu, 16 Apr 2020 00:37:45: 1000000 INFO @ Thu, 16 Apr 2020 00:37:49: 8000000 INFO @ Thu, 16 Apr 2020 00:37:50: 2000000 INFO @ Thu, 16 Apr 2020 00:37:54: 9000000 INFO @ Thu, 16 Apr 2020 00:37:55: 3000000 INFO @ Thu, 16 Apr 2020 00:38:00: 10000000 INFO @ Thu, 16 Apr 2020 00:38:00: 4000000 INFO @ Thu, 16 Apr 2020 00:38:05: 11000000 INFO @ Thu, 16 Apr 2020 00:38:05: 5000000 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 @ Thu, 16 Apr 2020 00:38:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592405/SRX2592405.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592405/SRX2592405.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592405/SRX2592405.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592405/SRX2592405.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 @ Thu, 16 Apr 2020 00:38:09: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:38:09: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:38:10: 12000000 INFO @ Thu, 16 Apr 2020 00:38:10: 6000000 INFO @ Thu, 16 Apr 2020 00:38:15: 1000000 INFO @ Thu, 16 Apr 2020 00:38:15: 13000000 INFO @ Thu, 16 Apr 2020 00:38:16: 7000000 INFO @ Thu, 16 Apr 2020 00:38:19: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:38:19: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:38:19: #1 total tags in treatment: 13637749 INFO @ Thu, 16 Apr 2020 00:38:19: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:38:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:38:19: #1 tags after filtering in treatment: 13637749 INFO @ Thu, 16 Apr 2020 00:38:19: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:38:19: #1 finished! INFO @ Thu, 16 Apr 2020 00:38:19: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:38:19: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:38:20: 2000000 INFO @ Thu, 16 Apr 2020 00:38:20: #2 number of paired peaks: 713 WARNING @ Thu, 16 Apr 2020 00:38:20: Fewer paired peaks (713) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 713 pairs to build model! INFO @ Thu, 16 Apr 2020 00:38:20: start model_add_line... INFO @ Thu, 16 Apr 2020 00:38:20: start X-correlation... INFO @ Thu, 16 Apr 2020 00:38:20: end of X-cor INFO @ Thu, 16 Apr 2020 00:38:20: #2 finished! INFO @ Thu, 16 Apr 2020 00:38:20: #2 predicted fragment length is 55 bps INFO @ Thu, 16 Apr 2020 00:38:20: #2 alternative fragment length(s) may be 55 bps INFO @ Thu, 16 Apr 2020 00:38:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592405/SRX2592405.05_model.r WARNING @ Thu, 16 Apr 2020 00:38:20: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:38:20: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Thu, 16 Apr 2020 00:38:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 00:38:20: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:38:20: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:38:21: 8000000 INFO @ Thu, 16 Apr 2020 00:38:25: 3000000 INFO @ Thu, 16 Apr 2020 00:38:26: 9000000 INFO @ Thu, 16 Apr 2020 00:38:30: 4000000 INFO @ Thu, 16 Apr 2020 00:38:31: 10000000 INFO @ Thu, 16 Apr 2020 00:38:35: 5000000 INFO @ Thu, 16 Apr 2020 00:38:36: 11000000 INFO @ Thu, 16 Apr 2020 00:38:41: 6000000 INFO @ Thu, 16 Apr 2020 00:38:42: 12000000 INFO @ Thu, 16 Apr 2020 00:38:46: 7000000 INFO @ Thu, 16 Apr 2020 00:38:46: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:38:47: 13000000 INFO @ Thu, 16 Apr 2020 00:38:50: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:38:50: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:38:50: #1 total tags in treatment: 13637749 INFO @ Thu, 16 Apr 2020 00:38:50: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:38:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:38:51: #1 tags after filtering in treatment: 13637749 INFO @ Thu, 16 Apr 2020 00:38:51: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:38:51: #1 finished! INFO @ Thu, 16 Apr 2020 00:38:51: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:38:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:38:51: 8000000 INFO @ Thu, 16 Apr 2020 00:38:52: #2 number of paired peaks: 713 WARNING @ Thu, 16 Apr 2020 00:38:52: Fewer paired peaks (713) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 713 pairs to build model! INFO @ Thu, 16 Apr 2020 00:38:52: start model_add_line... INFO @ Thu, 16 Apr 2020 00:38:52: start X-correlation... INFO @ Thu, 16 Apr 2020 00:38:52: end of X-cor INFO @ Thu, 16 Apr 2020 00:38:52: #2 finished! INFO @ Thu, 16 Apr 2020 00:38:52: #2 predicted fragment length is 55 bps INFO @ Thu, 16 Apr 2020 00:38:52: #2 alternative fragment length(s) may be 55 bps INFO @ Thu, 16 Apr 2020 00:38:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592405/SRX2592405.10_model.r WARNING @ Thu, 16 Apr 2020 00:38:52: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:38:52: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Thu, 16 Apr 2020 00:38:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 00:38:52: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:38:52: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:38:56: 9000000 INFO @ Thu, 16 Apr 2020 00:38:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592405/SRX2592405.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:38:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592405/SRX2592405.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:38:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592405/SRX2592405.05_summits.bed INFO @ Thu, 16 Apr 2020 00:38:59: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2284 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:39:01: 10000000 INFO @ Thu, 16 Apr 2020 00:39:06: 11000000 INFO @ Thu, 16 Apr 2020 00:39:12: 12000000 INFO @ Thu, 16 Apr 2020 00:39:17: 13000000 INFO @ Thu, 16 Apr 2020 00:39:18: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:39:20: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:39:20: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:39:20: #1 total tags in treatment: 13637749 INFO @ Thu, 16 Apr 2020 00:39:20: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:39:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:39:20: #1 tags after filtering in treatment: 13637749 INFO @ Thu, 16 Apr 2020 00:39:20: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:39:20: #1 finished! INFO @ Thu, 16 Apr 2020 00:39:20: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:39:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:39:21: #2 number of paired peaks: 713 WARNING @ Thu, 16 Apr 2020 00:39:21: Fewer paired peaks (713) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 713 pairs to build model! INFO @ Thu, 16 Apr 2020 00:39:21: start model_add_line... INFO @ Thu, 16 Apr 2020 00:39:21: start X-correlation... INFO @ Thu, 16 Apr 2020 00:39:21: end of X-cor INFO @ Thu, 16 Apr 2020 00:39:21: #2 finished! INFO @ Thu, 16 Apr 2020 00:39:21: #2 predicted fragment length is 55 bps INFO @ Thu, 16 Apr 2020 00:39:21: #2 alternative fragment length(s) may be 55 bps INFO @ Thu, 16 Apr 2020 00:39:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592405/SRX2592405.20_model.r WARNING @ Thu, 16 Apr 2020 00:39:21: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:39:21: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Thu, 16 Apr 2020 00:39:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 00:39:21: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:39:21: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:39:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592405/SRX2592405.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:39:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592405/SRX2592405.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:39:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592405/SRX2592405.10_summits.bed INFO @ Thu, 16 Apr 2020 00:39:30: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1483 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:39:48: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:40:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592405/SRX2592405.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:40:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592405/SRX2592405.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:40:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592405/SRX2592405.20_summits.bed INFO @ Thu, 16 Apr 2020 00:40:01: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (909 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。