Job ID = 5720709 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,994,004 reads read : 21,994,004 reads written : 21,994,004 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR7253453.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: 00:05:00 21994004 reads; of these: 21994004 (100.00%) were unpaired; of these: 2355971 (10.71%) aligned 0 times 15494005 (70.45%) aligned exactly 1 time 4144028 (18.84%) aligned >1 times 89.29% overall alignment rate Time searching: 00:05:00 Overall time: 00:05:00 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_rmdupse_core] 3172360 / 19638033 = 0.1615 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 01:09:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158173/SRX4158173.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158173/SRX4158173.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158173/SRX4158173.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158173/SRX4158173.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 01:09:11: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:09:11: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:09:17: 1000000 INFO @ Thu, 16 Apr 2020 01:09:24: 2000000 INFO @ Thu, 16 Apr 2020 01:09:30: 3000000 INFO @ Thu, 16 Apr 2020 01:09:37: 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 @ Thu, 16 Apr 2020 01:09:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158173/SRX4158173.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158173/SRX4158173.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158173/SRX4158173.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158173/SRX4158173.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 01:09:41: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:09:41: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:09:43: 5000000 INFO @ Thu, 16 Apr 2020 01:09:48: 1000000 INFO @ Thu, 16 Apr 2020 01:09:50: 6000000 INFO @ Thu, 16 Apr 2020 01:09:55: 2000000 INFO @ Thu, 16 Apr 2020 01:09:57: 7000000 INFO @ Thu, 16 Apr 2020 01:10:02: 3000000 INFO @ Thu, 16 Apr 2020 01:10:04: 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 @ Thu, 16 Apr 2020 01:10:09: 4000000 INFO @ Thu, 16 Apr 2020 01:10:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158173/SRX4158173.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158173/SRX4158173.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158173/SRX4158173.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158173/SRX4158173.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 01:10:11: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:10:11: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:10:11: 9000000 INFO @ Thu, 16 Apr 2020 01:10:17: 5000000 INFO @ Thu, 16 Apr 2020 01:10:18: 1000000 INFO @ Thu, 16 Apr 2020 01:10:18: 10000000 INFO @ Thu, 16 Apr 2020 01:10:24: 6000000 INFO @ Thu, 16 Apr 2020 01:10:25: 2000000 INFO @ Thu, 16 Apr 2020 01:10:25: 11000000 INFO @ Thu, 16 Apr 2020 01:10:31: 7000000 INFO @ Thu, 16 Apr 2020 01:10:32: 3000000 INFO @ Thu, 16 Apr 2020 01:10:32: 12000000 INFO @ Thu, 16 Apr 2020 01:10:38: 8000000 INFO @ Thu, 16 Apr 2020 01:10:39: 13000000 INFO @ Thu, 16 Apr 2020 01:10:39: 4000000 INFO @ Thu, 16 Apr 2020 01:10:45: 9000000 INFO @ Thu, 16 Apr 2020 01:10:46: 14000000 INFO @ Thu, 16 Apr 2020 01:10:46: 5000000 INFO @ Thu, 16 Apr 2020 01:10:52: 10000000 INFO @ Thu, 16 Apr 2020 01:10:53: 15000000 INFO @ Thu, 16 Apr 2020 01:10:53: 6000000 INFO @ Thu, 16 Apr 2020 01:10:59: 11000000 INFO @ Thu, 16 Apr 2020 01:11:00: 16000000 INFO @ Thu, 16 Apr 2020 01:11:00: 7000000 INFO @ Thu, 16 Apr 2020 01:11:03: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:11:03: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:11:03: #1 total tags in treatment: 16465673 INFO @ Thu, 16 Apr 2020 01:11:03: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:11:03: #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 01:11:03: #1 tags after filtering in treatment: 16465673 INFO @ Thu, 16 Apr 2020 01:11:03: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:11:03: #1 finished! INFO @ Thu, 16 Apr 2020 01:11:03: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:11:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:11:04: #2 number of paired peaks: 113 WARNING @ Thu, 16 Apr 2020 01:11:04: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Thu, 16 Apr 2020 01:11:04: start model_add_line... INFO @ Thu, 16 Apr 2020 01:11:04: start X-correlation... INFO @ Thu, 16 Apr 2020 01:11:04: end of X-cor INFO @ Thu, 16 Apr 2020 01:11:04: #2 finished! INFO @ Thu, 16 Apr 2020 01:11:04: #2 predicted fragment length is 50 bps INFO @ Thu, 16 Apr 2020 01:11:04: #2 alternative fragment length(s) may be 0,50,119,165,214,407,443,468,475,519,542,564 bps INFO @ Thu, 16 Apr 2020 01:11:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158173/SRX4158173.05_model.r WARNING @ Thu, 16 Apr 2020 01:11:04: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:11:04: #2 You may need to consider one of the other alternative d(s): 0,50,119,165,214,407,443,468,475,519,542,564 WARNING @ Thu, 16 Apr 2020 01:11:04: #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 01:11:04: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:11:04: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:11:06: 12000000 INFO @ Thu, 16 Apr 2020 01:11:07: 8000000 INFO @ Thu, 16 Apr 2020 01:11:13: 13000000 INFO @ Thu, 16 Apr 2020 01:11:13: 9000000 INFO @ Thu, 16 Apr 2020 01:11:19: 14000000 INFO @ Thu, 16 Apr 2020 01:11:20: 10000000 INFO @ Thu, 16 Apr 2020 01:11:26: 15000000 INFO @ Thu, 16 Apr 2020 01:11:27: 11000000 INFO @ Thu, 16 Apr 2020 01:11:33: 16000000 INFO @ Thu, 16 Apr 2020 01:11:33: 12000000 INFO @ Thu, 16 Apr 2020 01:11:35: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:11:36: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:11:36: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:11:36: #1 total tags in treatment: 16465673 INFO @ Thu, 16 Apr 2020 01:11:36: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:11:36: #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 01:11:36: #1 tags after filtering in treatment: 16465673 INFO @ Thu, 16 Apr 2020 01:11:36: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:11:36: #1 finished! INFO @ Thu, 16 Apr 2020 01:11:36: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:11:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:11:38: #2 number of paired peaks: 113 WARNING @ Thu, 16 Apr 2020 01:11:38: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Thu, 16 Apr 2020 01:11:38: start model_add_line... INFO @ Thu, 16 Apr 2020 01:11:38: start X-correlation... INFO @ Thu, 16 Apr 2020 01:11:38: end of X-cor INFO @ Thu, 16 Apr 2020 01:11:38: #2 finished! INFO @ Thu, 16 Apr 2020 01:11:38: #2 predicted fragment length is 50 bps INFO @ Thu, 16 Apr 2020 01:11:38: #2 alternative fragment length(s) may be 0,50,119,165,214,407,443,468,475,519,542,564 bps INFO @ Thu, 16 Apr 2020 01:11:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158173/SRX4158173.10_model.r WARNING @ Thu, 16 Apr 2020 01:11:38: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:11:38: #2 You may need to consider one of the other alternative d(s): 0,50,119,165,214,407,443,468,475,519,542,564 WARNING @ Thu, 16 Apr 2020 01:11:38: #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 01:11:38: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:11:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:11:40: 13000000 INFO @ Thu, 16 Apr 2020 01:11:46: 14000000 INFO @ Thu, 16 Apr 2020 01:11:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158173/SRX4158173.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:11:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158173/SRX4158173.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:11:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158173/SRX4158173.05_summits.bed INFO @ Thu, 16 Apr 2020 01:11:50: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (544 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:11:53: 15000000 INFO @ Thu, 16 Apr 2020 01:12:00: 16000000 INFO @ Thu, 16 Apr 2020 01:12:03: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:12:03: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:12:03: #1 total tags in treatment: 16465673 INFO @ Thu, 16 Apr 2020 01:12:03: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:12:03: #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 01:12:03: #1 tags after filtering in treatment: 16465673 INFO @ Thu, 16 Apr 2020 01:12:03: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:12:03: #1 finished! INFO @ Thu, 16 Apr 2020 01:12:03: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:12:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:12:04: #2 number of paired peaks: 113 WARNING @ Thu, 16 Apr 2020 01:12:04: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Thu, 16 Apr 2020 01:12:04: start model_add_line... INFO @ Thu, 16 Apr 2020 01:12:04: start X-correlation... INFO @ Thu, 16 Apr 2020 01:12:04: end of X-cor INFO @ Thu, 16 Apr 2020 01:12:04: #2 finished! INFO @ Thu, 16 Apr 2020 01:12:04: #2 predicted fragment length is 50 bps INFO @ Thu, 16 Apr 2020 01:12:04: #2 alternative fragment length(s) may be 0,50,119,165,214,407,443,468,475,519,542,564 bps INFO @ Thu, 16 Apr 2020 01:12:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158173/SRX4158173.20_model.r WARNING @ Thu, 16 Apr 2020 01:12:04: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:12:04: #2 You may need to consider one of the other alternative d(s): 0,50,119,165,214,407,443,468,475,519,542,564 WARNING @ Thu, 16 Apr 2020 01:12:04: #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 01:12:04: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:12:04: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:12:07: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:12:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158173/SRX4158173.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:12:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158173/SRX4158173.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:12:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158173/SRX4158173.10_summits.bed INFO @ Thu, 16 Apr 2020 01:12:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (187 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:12:34: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:12:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158173/SRX4158173.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:12:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158173/SRX4158173.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:12:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158173/SRX4158173.20_summits.bed INFO @ Thu, 16 Apr 2020 01:12:49: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (102 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。