Job ID = 6454894 SRX = SRX2592482 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:26:44 prefetch.2.10.7: 1) Downloading 'SRR5289759'... 2020-06-21T09:26:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:32:25 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:32:25 prefetch.2.10.7: 1) 'SRR5289759' was downloaded successfully Read 20714179 spots for SRR5289759/SRR5289759.sra Written 20714179 spots for SRR5289759/SRR5289759.sra 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: 00:05:17 20714179 reads; of these: 20714179 (100.00%) were unpaired; of these: 4467562 (21.57%) aligned 0 times 12501625 (60.35%) aligned exactly 1 time 3744992 (18.08%) aligned >1 times 78.43% overall alignment rate Time searching: 00:05:18 Overall time: 00:05:18 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 2540400 / 16246617 = 0.1564 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 @ Sun, 21 Jun 2020 18:43:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592482/SRX2592482.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592482/SRX2592482.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592482/SRX2592482.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592482/SRX2592482.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 @ Sun, 21 Jun 2020 18:43:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:43:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:43:48: 1000000 INFO @ Sun, 21 Jun 2020 18:43:54: 2000000 INFO @ Sun, 21 Jun 2020 18:44:00: 3000000 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 @ Sun, 21 Jun 2020 18:44:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592482/SRX2592482.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592482/SRX2592482.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592482/SRX2592482.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592482/SRX2592482.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 @ Sun, 21 Jun 2020 18:44:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:44:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:44:06: 4000000 INFO @ Sun, 21 Jun 2020 18:44:12: 1000000 INFO @ Sun, 21 Jun 2020 18:44:13: 5000000 INFO @ Sun, 21 Jun 2020 18:44:19: 2000000 INFO @ Sun, 21 Jun 2020 18:44:19: 6000000 INFO @ Sun, 21 Jun 2020 18:44:25: 3000000 INFO @ Sun, 21 Jun 2020 18:44:26: 7000000 INFO @ Sun, 21 Jun 2020 18:44:32: 4000000 INFO @ Sun, 21 Jun 2020 18:44:32: 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 @ Sun, 21 Jun 2020 18:44:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592482/SRX2592482.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592482/SRX2592482.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592482/SRX2592482.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592482/SRX2592482.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 @ Sun, 21 Jun 2020 18:44:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:44:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:44:38: 5000000 INFO @ Sun, 21 Jun 2020 18:44:39: 9000000 INFO @ Sun, 21 Jun 2020 18:44:43: 1000000 INFO @ Sun, 21 Jun 2020 18:44:44: 6000000 INFO @ Sun, 21 Jun 2020 18:44:45: 10000000 INFO @ Sun, 21 Jun 2020 18:44:49: 2000000 INFO @ Sun, 21 Jun 2020 18:44:51: 7000000 INFO @ Sun, 21 Jun 2020 18:44:52: 11000000 INFO @ Sun, 21 Jun 2020 18:44:56: 3000000 INFO @ Sun, 21 Jun 2020 18:44:57: 8000000 INFO @ Sun, 21 Jun 2020 18:44:59: 12000000 INFO @ Sun, 21 Jun 2020 18:45:02: 4000000 INFO @ Sun, 21 Jun 2020 18:45:03: 9000000 INFO @ Sun, 21 Jun 2020 18:45:05: 13000000 INFO @ Sun, 21 Jun 2020 18:45:09: 5000000 INFO @ Sun, 21 Jun 2020 18:45:09: 10000000 INFO @ Sun, 21 Jun 2020 18:45:10: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:45:10: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:45:10: #1 total tags in treatment: 13706217 INFO @ Sun, 21 Jun 2020 18:45:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:45:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:45:11: #1 tags after filtering in treatment: 13706112 INFO @ Sun, 21 Jun 2020 18:45:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:45:11: #1 finished! INFO @ Sun, 21 Jun 2020 18:45:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:45:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:45:12: #2 number of paired peaks: 339 WARNING @ Sun, 21 Jun 2020 18:45:12: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Sun, 21 Jun 2020 18:45:12: start model_add_line... INFO @ Sun, 21 Jun 2020 18:45:12: start X-correlation... INFO @ Sun, 21 Jun 2020 18:45:12: end of X-cor INFO @ Sun, 21 Jun 2020 18:45:12: #2 finished! INFO @ Sun, 21 Jun 2020 18:45:12: #2 predicted fragment length is 93 bps INFO @ Sun, 21 Jun 2020 18:45:12: #2 alternative fragment length(s) may be 93,580 bps INFO @ Sun, 21 Jun 2020 18:45:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592482/SRX2592482.05_model.r WARNING @ Sun, 21 Jun 2020 18:45:12: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:45:12: #2 You may need to consider one of the other alternative d(s): 93,580 WARNING @ Sun, 21 Jun 2020 18:45:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:45:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:45:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:45:15: 6000000 INFO @ Sun, 21 Jun 2020 18:45:16: 11000000 INFO @ Sun, 21 Jun 2020 18:45:21: 7000000 INFO @ Sun, 21 Jun 2020 18:45:22: 12000000 INFO @ Sun, 21 Jun 2020 18:45:28: 8000000 INFO @ Sun, 21 Jun 2020 18:45:28: 13000000 INFO @ Sun, 21 Jun 2020 18:45:33: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:45:33: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:45:33: #1 total tags in treatment: 13706217 INFO @ Sun, 21 Jun 2020 18:45:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:45:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:45:34: #1 tags after filtering in treatment: 13706112 INFO @ Sun, 21 Jun 2020 18:45:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:45:34: #1 finished! INFO @ Sun, 21 Jun 2020 18:45:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:45:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:45:34: 9000000 INFO @ Sun, 21 Jun 2020 18:45:35: #2 number of paired peaks: 339 WARNING @ Sun, 21 Jun 2020 18:45:35: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Sun, 21 Jun 2020 18:45:35: start model_add_line... INFO @ Sun, 21 Jun 2020 18:45:35: start X-correlation... INFO @ Sun, 21 Jun 2020 18:45:35: end of X-cor INFO @ Sun, 21 Jun 2020 18:45:35: #2 finished! INFO @ Sun, 21 Jun 2020 18:45:35: #2 predicted fragment length is 93 bps INFO @ Sun, 21 Jun 2020 18:45:35: #2 alternative fragment length(s) may be 93,580 bps INFO @ Sun, 21 Jun 2020 18:45:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592482/SRX2592482.10_model.r WARNING @ Sun, 21 Jun 2020 18:45:35: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:45:35: #2 You may need to consider one of the other alternative d(s): 93,580 WARNING @ Sun, 21 Jun 2020 18:45:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:45:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:45:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:45:40: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:45:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:45:46: 11000000 INFO @ Sun, 21 Jun 2020 18:45:52: 12000000 INFO @ Sun, 21 Jun 2020 18:45:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592482/SRX2592482.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:45:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592482/SRX2592482.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:45:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592482/SRX2592482.05_summits.bed INFO @ Sun, 21 Jun 2020 18:45:57: Done! INFO @ Sun, 21 Jun 2020 18:45:58: 13000000 pass1 - making usageList (583 chroms): 2 millis pass2 - checking and writing primary data (4325 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:46:02: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:46:02: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:46:02: #1 total tags in treatment: 13706217 INFO @ Sun, 21 Jun 2020 18:46:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:46:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:46:03: #1 tags after filtering in treatment: 13706112 INFO @ Sun, 21 Jun 2020 18:46:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:46:03: #1 finished! INFO @ Sun, 21 Jun 2020 18:46:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:46:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:46:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:46:04: #2 number of paired peaks: 339 WARNING @ Sun, 21 Jun 2020 18:46:04: Fewer paired peaks (339) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 339 pairs to build model! INFO @ Sun, 21 Jun 2020 18:46:04: start model_add_line... INFO @ Sun, 21 Jun 2020 18:46:04: start X-correlation... INFO @ Sun, 21 Jun 2020 18:46:04: end of X-cor INFO @ Sun, 21 Jun 2020 18:46:04: #2 finished! INFO @ Sun, 21 Jun 2020 18:46:04: #2 predicted fragment length is 93 bps INFO @ Sun, 21 Jun 2020 18:46:04: #2 alternative fragment length(s) may be 93,580 bps INFO @ Sun, 21 Jun 2020 18:46:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592482/SRX2592482.20_model.r WARNING @ Sun, 21 Jun 2020 18:46:04: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:46:04: #2 You may need to consider one of the other alternative d(s): 93,580 WARNING @ Sun, 21 Jun 2020 18:46:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:46:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:46:04: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:46:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592482/SRX2592482.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:46:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592482/SRX2592482.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:46:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592482/SRX2592482.10_summits.bed INFO @ Sun, 21 Jun 2020 18:46:17: Done! pass1 - making usageList (374 chroms): 1 millis pass2 - checking and writing primary data (1344 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:46:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:46:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592482/SRX2592482.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:46:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592482/SRX2592482.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:46:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592482/SRX2592482.20_summits.bed INFO @ Sun, 21 Jun 2020 18:46:47: Done! pass1 - making usageList (172 chroms): 1 millis pass2 - checking and writing primary data (383 records, 4 fields): 6 millis CompletedMACS2peakCalling