Job ID = 6528008 SRX = SRX385809 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T14:03:07 prefetch.2.10.7: 1) Downloading 'SRR1041450'... 2020-06-29T14:03:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:06:34 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:06:34 prefetch.2.10.7: 1) 'SRR1041450' was downloaded successfully Read 27474174 spots for SRR1041450/SRR1041450.sra Written 27474174 spots for SRR1041450/SRR1041450.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: 00:09:35 27474174 reads; of these: 27474174 (100.00%) were unpaired; of these: 550878 (2.01%) aligned 0 times 19409023 (70.64%) aligned exactly 1 time 7514273 (27.35%) aligned >1 times 97.99% overall alignment rate Time searching: 00:09:35 Overall time: 00:09:35 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] 2999219 / 26923296 = 0.1114 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 @ Mon, 29 Jun 2020 23:31:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX385809/SRX385809.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX385809/SRX385809.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX385809/SRX385809.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX385809/SRX385809.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 @ Mon, 29 Jun 2020 23:31:04: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:31:04: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:31:11: 1000000 INFO @ Mon, 29 Jun 2020 23:31:18: 2000000 INFO @ Mon, 29 Jun 2020 23:31:25: 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 @ Mon, 29 Jun 2020 23:31:32: 4000000 INFO @ Mon, 29 Jun 2020 23:31:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX385809/SRX385809.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX385809/SRX385809.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX385809/SRX385809.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX385809/SRX385809.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 @ Mon, 29 Jun 2020 23:31:34: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:31:34: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:31:40: 5000000 INFO @ Mon, 29 Jun 2020 23:31:41: 1000000 INFO @ Mon, 29 Jun 2020 23:31:47: 6000000 INFO @ Mon, 29 Jun 2020 23:31:49: 2000000 INFO @ Mon, 29 Jun 2020 23:31:55: 7000000 INFO @ Mon, 29 Jun 2020 23:31:57: 3000000 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 @ Mon, 29 Jun 2020 23:32:03: 8000000 INFO @ Mon, 29 Jun 2020 23:32:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX385809/SRX385809.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX385809/SRX385809.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX385809/SRX385809.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX385809/SRX385809.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 @ Mon, 29 Jun 2020 23:32:04: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:32:04: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:32:04: 4000000 INFO @ Mon, 29 Jun 2020 23:32:11: 9000000 INFO @ Mon, 29 Jun 2020 23:32:12: 1000000 INFO @ Mon, 29 Jun 2020 23:32:12: 5000000 INFO @ Mon, 29 Jun 2020 23:32:19: 10000000 INFO @ Mon, 29 Jun 2020 23:32:20: 2000000 INFO @ Mon, 29 Jun 2020 23:32:20: 6000000 INFO @ Mon, 29 Jun 2020 23:32:27: 11000000 INFO @ Mon, 29 Jun 2020 23:32:28: 3000000 INFO @ Mon, 29 Jun 2020 23:32:29: 7000000 INFO @ Mon, 29 Jun 2020 23:32:34: 12000000 INFO @ Mon, 29 Jun 2020 23:32:35: 4000000 INFO @ Mon, 29 Jun 2020 23:32:37: 8000000 INFO @ Mon, 29 Jun 2020 23:32:42: 13000000 INFO @ Mon, 29 Jun 2020 23:32:43: 5000000 INFO @ Mon, 29 Jun 2020 23:32:44: 9000000 INFO @ Mon, 29 Jun 2020 23:32:50: 14000000 INFO @ Mon, 29 Jun 2020 23:32:51: 6000000 INFO @ Mon, 29 Jun 2020 23:32:52: 10000000 INFO @ Mon, 29 Jun 2020 23:32:58: 15000000 INFO @ Mon, 29 Jun 2020 23:32:59: 7000000 INFO @ Mon, 29 Jun 2020 23:33:00: 11000000 INFO @ Mon, 29 Jun 2020 23:33:06: 16000000 INFO @ Mon, 29 Jun 2020 23:33:07: 8000000 INFO @ Mon, 29 Jun 2020 23:33:08: 12000000 INFO @ Mon, 29 Jun 2020 23:33:14: 17000000 INFO @ Mon, 29 Jun 2020 23:33:15: 9000000 INFO @ Mon, 29 Jun 2020 23:33:16: 13000000 INFO @ Mon, 29 Jun 2020 23:33:22: 18000000 INFO @ Mon, 29 Jun 2020 23:33:22: 10000000 INFO @ Mon, 29 Jun 2020 23:33:23: 14000000 INFO @ Mon, 29 Jun 2020 23:33:30: 19000000 INFO @ Mon, 29 Jun 2020 23:33:30: 11000000 INFO @ Mon, 29 Jun 2020 23:33:31: 15000000 INFO @ Mon, 29 Jun 2020 23:33:38: 12000000 INFO @ Mon, 29 Jun 2020 23:33:38: 20000000 INFO @ Mon, 29 Jun 2020 23:33:39: 16000000 INFO @ Mon, 29 Jun 2020 23:33:46: 13000000 INFO @ Mon, 29 Jun 2020 23:33:46: 21000000 INFO @ Mon, 29 Jun 2020 23:33:46: 17000000 INFO @ Mon, 29 Jun 2020 23:33:53: 14000000 INFO @ Mon, 29 Jun 2020 23:33:54: 18000000 INFO @ Mon, 29 Jun 2020 23:33:54: 22000000 INFO @ Mon, 29 Jun 2020 23:34:01: 15000000 INFO @ Mon, 29 Jun 2020 23:34:02: 19000000 INFO @ Mon, 29 Jun 2020 23:34:02: 23000000 INFO @ Mon, 29 Jun 2020 23:34:09: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:34:10: #1 tag size is determined as 49 bps INFO @ Mon, 29 Jun 2020 23:34:10: #1 tag size = 49 INFO @ Mon, 29 Jun 2020 23:34:10: #1 total tags in treatment: 23924077 INFO @ Mon, 29 Jun 2020 23:34:10: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:34:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:34:10: 20000000 INFO @ Mon, 29 Jun 2020 23:34:10: #1 tags after filtering in treatment: 23924077 INFO @ Mon, 29 Jun 2020 23:34:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:34:10: #1 finished! INFO @ Mon, 29 Jun 2020 23:34:10: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:34:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:34:12: #2 number of paired peaks: 292 WARNING @ Mon, 29 Jun 2020 23:34:12: Fewer paired peaks (292) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 292 pairs to build model! INFO @ Mon, 29 Jun 2020 23:34:12: start model_add_line... INFO @ Mon, 29 Jun 2020 23:34:12: start X-correlation... INFO @ Mon, 29 Jun 2020 23:34:12: end of X-cor INFO @ Mon, 29 Jun 2020 23:34:12: #2 finished! INFO @ Mon, 29 Jun 2020 23:34:12: #2 predicted fragment length is 37 bps INFO @ Mon, 29 Jun 2020 23:34:12: #2 alternative fragment length(s) may be 3,37,527 bps INFO @ Mon, 29 Jun 2020 23:34:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX385809/SRX385809.05_model.r WARNING @ Mon, 29 Jun 2020 23:34:12: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:34:12: #2 You may need to consider one of the other alternative d(s): 3,37,527 WARNING @ Mon, 29 Jun 2020 23:34:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:34:12: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:34:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:34:16: 17000000 INFO @ Mon, 29 Jun 2020 23:34:18: 21000000 INFO @ Mon, 29 Jun 2020 23:34:24: 18000000 INFO @ Mon, 29 Jun 2020 23:34:26: 22000000 INFO @ Mon, 29 Jun 2020 23:34:31: 19000000 INFO @ Mon, 29 Jun 2020 23:34:33: 23000000 INFO @ Mon, 29 Jun 2020 23:34:39: 20000000 INFO @ Mon, 29 Jun 2020 23:34:40: #1 tag size is determined as 49 bps INFO @ Mon, 29 Jun 2020 23:34:40: #1 tag size = 49 INFO @ Mon, 29 Jun 2020 23:34:40: #1 total tags in treatment: 23924077 INFO @ Mon, 29 Jun 2020 23:34:40: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:34:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:34:41: #1 tags after filtering in treatment: 23924077 INFO @ Mon, 29 Jun 2020 23:34:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:34:41: #1 finished! INFO @ Mon, 29 Jun 2020 23:34:41: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:34:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:34:42: #2 number of paired peaks: 292 WARNING @ Mon, 29 Jun 2020 23:34:42: Fewer paired peaks (292) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 292 pairs to build model! INFO @ Mon, 29 Jun 2020 23:34:42: start model_add_line... INFO @ Mon, 29 Jun 2020 23:34:42: start X-correlation... INFO @ Mon, 29 Jun 2020 23:34:43: end of X-cor INFO @ Mon, 29 Jun 2020 23:34:43: #2 finished! INFO @ Mon, 29 Jun 2020 23:34:43: #2 predicted fragment length is 37 bps INFO @ Mon, 29 Jun 2020 23:34:43: #2 alternative fragment length(s) may be 3,37,527 bps INFO @ Mon, 29 Jun 2020 23:34:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX385809/SRX385809.10_model.r WARNING @ Mon, 29 Jun 2020 23:34:43: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:34:43: #2 You may need to consider one of the other alternative d(s): 3,37,527 WARNING @ Mon, 29 Jun 2020 23:34:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:34:43: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:34:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:34:47: 21000000 INFO @ Mon, 29 Jun 2020 23:34:54: 22000000 INFO @ Mon, 29 Jun 2020 23:34:58: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:35:01: 23000000 BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:35:07: #1 tag size is determined as 49 bps INFO @ Mon, 29 Jun 2020 23:35:07: #1 tag size = 49 INFO @ Mon, 29 Jun 2020 23:35:07: #1 total tags in treatment: 23924077 INFO @ Mon, 29 Jun 2020 23:35:07: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:35:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:35:08: #1 tags after filtering in treatment: 23924077 INFO @ Mon, 29 Jun 2020 23:35:08: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:35:08: #1 finished! INFO @ Mon, 29 Jun 2020 23:35:08: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:35:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:35:09: #2 number of paired peaks: 292 WARNING @ Mon, 29 Jun 2020 23:35:09: Fewer paired peaks (292) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 292 pairs to build model! INFO @ Mon, 29 Jun 2020 23:35:09: start model_add_line... INFO @ Mon, 29 Jun 2020 23:35:09: start X-correlation... INFO @ Mon, 29 Jun 2020 23:35:09: end of X-cor INFO @ Mon, 29 Jun 2020 23:35:09: #2 finished! INFO @ Mon, 29 Jun 2020 23:35:09: #2 predicted fragment length is 37 bps INFO @ Mon, 29 Jun 2020 23:35:09: #2 alternative fragment length(s) may be 3,37,527 bps INFO @ Mon, 29 Jun 2020 23:35:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX385809/SRX385809.20_model.r WARNING @ Mon, 29 Jun 2020 23:35:09: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:35:09: #2 You may need to consider one of the other alternative d(s): 3,37,527 WARNING @ Mon, 29 Jun 2020 23:35:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:35:09: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:35:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:35:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX385809/SRX385809.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:35:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX385809/SRX385809.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:35:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX385809/SRX385809.05_summits.bed INFO @ Mon, 29 Jun 2020 23:35:20: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3473 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:35:23: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:35:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX385809/SRX385809.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:35:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX385809/SRX385809.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:35:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX385809/SRX385809.10_summits.bed INFO @ Mon, 29 Jun 2020 23:35:43: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1974 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:35:50: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:36:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX385809/SRX385809.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:36:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX385809/SRX385809.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:36:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX385809/SRX385809.20_summits.bed INFO @ Mon, 29 Jun 2020 23:36:10: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1130 records, 4 fields): 3 millis CompletedMACS2peakCalling