Job ID = 5721093 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 31,048,958 reads read : 62,097,916 reads written : 31,048,958 reads 0-length : 31,048,958 rm: cannot remove ‘[DSE]RR*’: 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: 00:12:06 31048958 reads; of these: 31048958 (100.00%) were unpaired; of these: 2963481 (9.54%) aligned 0 times 20021778 (64.48%) aligned exactly 1 time 8063699 (25.97%) aligned >1 times 90.46% overall alignment rate Time searching: 00:12:06 Overall time: 00:12:06 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] 6250658 / 28085477 = 0.2226 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 05:02:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6685748/SRX6685748.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6685748/SRX6685748.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6685748/SRX6685748.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6685748/SRX6685748.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 05:02:25: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:02:25: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:02:30: 1000000 INFO @ Thu, 16 Apr 2020 05:02:35: 2000000 INFO @ Thu, 16 Apr 2020 05:02:40: 3000000 INFO @ Thu, 16 Apr 2020 05:02:46: 4000000 INFO @ Thu, 16 Apr 2020 05:02:51: 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 05:02:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6685748/SRX6685748.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6685748/SRX6685748.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6685748/SRX6685748.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6685748/SRX6685748.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 05:02:55: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:02:55: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:02:56: 6000000 INFO @ Thu, 16 Apr 2020 05:03:00: 1000000 INFO @ Thu, 16 Apr 2020 05:03:01: 7000000 INFO @ Thu, 16 Apr 2020 05:03:05: 2000000 INFO @ Thu, 16 Apr 2020 05:03:06: 8000000 INFO @ Thu, 16 Apr 2020 05:03:11: 3000000 INFO @ Thu, 16 Apr 2020 05:03:11: 9000000 INFO @ Thu, 16 Apr 2020 05:03:16: 4000000 INFO @ Thu, 16 Apr 2020 05:03:16: 10000000 INFO @ Thu, 16 Apr 2020 05:03:21: 5000000 INFO @ Thu, 16 Apr 2020 05:03:21: 11000000 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 05:03:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6685748/SRX6685748.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6685748/SRX6685748.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6685748/SRX6685748.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6685748/SRX6685748.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 05:03:25: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:03:25: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:03:26: 6000000 INFO @ Thu, 16 Apr 2020 05:03:26: 12000000 INFO @ Thu, 16 Apr 2020 05:03:31: 1000000 INFO @ Thu, 16 Apr 2020 05:03:31: 13000000 INFO @ Thu, 16 Apr 2020 05:03:31: 7000000 INFO @ Thu, 16 Apr 2020 05:03:36: 2000000 INFO @ Thu, 16 Apr 2020 05:03:36: 14000000 INFO @ Thu, 16 Apr 2020 05:03:36: 8000000 INFO @ Thu, 16 Apr 2020 05:03:41: 3000000 INFO @ Thu, 16 Apr 2020 05:03:41: 15000000 INFO @ Thu, 16 Apr 2020 05:03:41: 9000000 INFO @ Thu, 16 Apr 2020 05:03:46: 4000000 INFO @ Thu, 16 Apr 2020 05:03:46: 16000000 INFO @ Thu, 16 Apr 2020 05:03:46: 10000000 INFO @ Thu, 16 Apr 2020 05:03:51: 5000000 INFO @ Thu, 16 Apr 2020 05:03:51: 17000000 INFO @ Thu, 16 Apr 2020 05:03:51: 11000000 INFO @ Thu, 16 Apr 2020 05:03:56: 12000000 INFO @ Thu, 16 Apr 2020 05:03:56: 18000000 INFO @ Thu, 16 Apr 2020 05:03:56: 6000000 INFO @ Thu, 16 Apr 2020 05:04:01: 13000000 INFO @ Thu, 16 Apr 2020 05:04:01: 19000000 INFO @ Thu, 16 Apr 2020 05:04:02: 7000000 INFO @ Thu, 16 Apr 2020 05:04:06: 14000000 INFO @ Thu, 16 Apr 2020 05:04:06: 20000000 INFO @ Thu, 16 Apr 2020 05:04:07: 8000000 INFO @ Thu, 16 Apr 2020 05:04:11: 15000000 INFO @ Thu, 16 Apr 2020 05:04:11: 21000000 INFO @ Thu, 16 Apr 2020 05:04:12: 9000000 INFO @ Thu, 16 Apr 2020 05:04:16: #1 tag size is determined as 74 bps INFO @ Thu, 16 Apr 2020 05:04:16: #1 tag size = 74 INFO @ Thu, 16 Apr 2020 05:04:16: #1 total tags in treatment: 21834819 INFO @ Thu, 16 Apr 2020 05:04:16: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:04:16: #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 05:04:16: #1 tags after filtering in treatment: 21834819 INFO @ Thu, 16 Apr 2020 05:04:16: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 05:04:16: #1 finished! INFO @ Thu, 16 Apr 2020 05:04:16: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:04:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:04:16: 16000000 INFO @ Thu, 16 Apr 2020 05:04:17: 10000000 INFO @ Thu, 16 Apr 2020 05:04:18: #2 number of paired peaks: 671 WARNING @ Thu, 16 Apr 2020 05:04:18: Fewer paired peaks (671) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 671 pairs to build model! INFO @ Thu, 16 Apr 2020 05:04:18: start model_add_line... INFO @ Thu, 16 Apr 2020 05:04:18: start X-correlation... INFO @ Thu, 16 Apr 2020 05:04:18: end of X-cor INFO @ Thu, 16 Apr 2020 05:04:18: #2 finished! INFO @ Thu, 16 Apr 2020 05:04:18: #2 predicted fragment length is 125 bps INFO @ Thu, 16 Apr 2020 05:04:18: #2 alternative fragment length(s) may be 125 bps INFO @ Thu, 16 Apr 2020 05:04:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6685748/SRX6685748.05_model.r WARNING @ Thu, 16 Apr 2020 05:04:18: #2 Since the d (125) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:04:18: #2 You may need to consider one of the other alternative d(s): 125 WARNING @ Thu, 16 Apr 2020 05:04:18: #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 05:04:18: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:04:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:04:22: 17000000 INFO @ Thu, 16 Apr 2020 05:04:22: 11000000 INFO @ Thu, 16 Apr 2020 05:04:27: 18000000 INFO @ Thu, 16 Apr 2020 05:04:27: 12000000 INFO @ Thu, 16 Apr 2020 05:04:32: 19000000 INFO @ Thu, 16 Apr 2020 05:04:32: 13000000 INFO @ Thu, 16 Apr 2020 05:04:37: 20000000 INFO @ Thu, 16 Apr 2020 05:04:37: 14000000 INFO @ Thu, 16 Apr 2020 05:04:42: 21000000 INFO @ Thu, 16 Apr 2020 05:04:42: 15000000 INFO @ Thu, 16 Apr 2020 05:04:46: #1 tag size is determined as 74 bps INFO @ Thu, 16 Apr 2020 05:04:46: #1 tag size = 74 INFO @ Thu, 16 Apr 2020 05:04:46: #1 total tags in treatment: 21834819 INFO @ Thu, 16 Apr 2020 05:04:46: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:04:46: #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 05:04:47: #1 tags after filtering in treatment: 21834819 INFO @ Thu, 16 Apr 2020 05:04:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 05:04:47: #1 finished! INFO @ Thu, 16 Apr 2020 05:04:47: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:04:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:04:47: 16000000 INFO @ Thu, 16 Apr 2020 05:04:48: #2 number of paired peaks: 671 WARNING @ Thu, 16 Apr 2020 05:04:48: Fewer paired peaks (671) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 671 pairs to build model! INFO @ Thu, 16 Apr 2020 05:04:48: start model_add_line... INFO @ Thu, 16 Apr 2020 05:04:48: start X-correlation... INFO @ Thu, 16 Apr 2020 05:04:48: end of X-cor INFO @ Thu, 16 Apr 2020 05:04:48: #2 finished! INFO @ Thu, 16 Apr 2020 05:04:48: #2 predicted fragment length is 125 bps INFO @ Thu, 16 Apr 2020 05:04:48: #2 alternative fragment length(s) may be 125 bps INFO @ Thu, 16 Apr 2020 05:04:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6685748/SRX6685748.10_model.r WARNING @ Thu, 16 Apr 2020 05:04:48: #2 Since the d (125) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:04:48: #2 You may need to consider one of the other alternative d(s): 125 WARNING @ Thu, 16 Apr 2020 05:04:48: #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 05:04:48: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:04:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:04:52: 17000000 INFO @ Thu, 16 Apr 2020 05:04:57: 18000000 INFO @ Thu, 16 Apr 2020 05:05:01: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:05:02: 19000000 INFO @ Thu, 16 Apr 2020 05:05:07: 20000000 INFO @ Thu, 16 Apr 2020 05:05:12: 21000000 INFO @ Thu, 16 Apr 2020 05:05:17: #1 tag size is determined as 74 bps INFO @ Thu, 16 Apr 2020 05:05:17: #1 tag size = 74 INFO @ Thu, 16 Apr 2020 05:05:17: #1 total tags in treatment: 21834819 INFO @ Thu, 16 Apr 2020 05:05:17: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:05:17: #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 05:05:17: #1 tags after filtering in treatment: 21834819 INFO @ Thu, 16 Apr 2020 05:05:17: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 05:05:17: #1 finished! INFO @ Thu, 16 Apr 2020 05:05:17: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:05:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:05:19: #2 number of paired peaks: 671 WARNING @ Thu, 16 Apr 2020 05:05:19: Fewer paired peaks (671) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 671 pairs to build model! INFO @ Thu, 16 Apr 2020 05:05:19: start model_add_line... INFO @ Thu, 16 Apr 2020 05:05:19: start X-correlation... INFO @ Thu, 16 Apr 2020 05:05:19: end of X-cor INFO @ Thu, 16 Apr 2020 05:05:19: #2 finished! INFO @ Thu, 16 Apr 2020 05:05:19: #2 predicted fragment length is 125 bps INFO @ Thu, 16 Apr 2020 05:05:19: #2 alternative fragment length(s) may be 125 bps INFO @ Thu, 16 Apr 2020 05:05:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6685748/SRX6685748.20_model.r WARNING @ Thu, 16 Apr 2020 05:05:19: #2 Since the d (125) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 05:05:19: #2 You may need to consider one of the other alternative d(s): 125 WARNING @ Thu, 16 Apr 2020 05:05:19: #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 05:05:19: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:05:19: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:05:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6685748/SRX6685748.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:05:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6685748/SRX6685748.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:05:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6685748/SRX6685748.05_summits.bed INFO @ Thu, 16 Apr 2020 05:05:22: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8518 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:05:31: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:05:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6685748/SRX6685748.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:05:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6685748/SRX6685748.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:05:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6685748/SRX6685748.10_summits.bed INFO @ Thu, 16 Apr 2020 05:05:52: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6576 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:06:02: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:06:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6685748/SRX6685748.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:06:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6685748/SRX6685748.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:06:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6685748/SRX6685748.20_summits.bed INFO @ Thu, 16 Apr 2020 05:06:23: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4575 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。