Job ID = 6454982 SRX = SRX2618521 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:31:44 prefetch.2.10.7: 1) Downloading 'SRR5319075'... 2020-06-21T09:31:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:33:27 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:33:28 prefetch.2.10.7: 'SRR5319075' is valid 2020-06-21T09:33:28 prefetch.2.10.7: 1) 'SRR5319075' was downloaded successfully 2020-06-21T09:33:28 prefetch.2.10.7: 'SRR5319075' has 0 unresolved dependencies Read 15535946 spots for SRR5319075/SRR5319075.sra Written 15535946 spots for SRR5319075/SRR5319075.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: 00:03:59 15535946 reads; of these: 15535946 (100.00%) were unpaired; of these: 888909 (5.72%) aligned 0 times 11117791 (71.56%) aligned exactly 1 time 3529246 (22.72%) aligned >1 times 94.28% overall alignment rate Time searching: 00:03:59 Overall time: 00:03:59 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] 1960630 / 14647037 = 0.1339 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 18:42:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618521/SRX2618521.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618521/SRX2618521.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618521/SRX2618521.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618521/SRX2618521.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 18:42:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:42:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:42:10: 1000000 INFO @ Sun, 21 Jun 2020 18:42:16: 2000000 INFO @ Sun, 21 Jun 2020 18:42:21: 3000000 INFO @ Sun, 21 Jun 2020 18:42:27: 4000000 INFO @ Sun, 21 Jun 2020 18:42:32: 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 @ Sun, 21 Jun 2020 18:42:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618521/SRX2618521.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618521/SRX2618521.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618521/SRX2618521.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618521/SRX2618521.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 18:42:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:42:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:42:38: 6000000 INFO @ Sun, 21 Jun 2020 18:42:41: 1000000 INFO @ Sun, 21 Jun 2020 18:42:44: 7000000 INFO @ Sun, 21 Jun 2020 18:42:47: 2000000 INFO @ Sun, 21 Jun 2020 18:42:50: 8000000 INFO @ Sun, 21 Jun 2020 18:42:53: 3000000 INFO @ Sun, 21 Jun 2020 18:42:56: 9000000 INFO @ Sun, 21 Jun 2020 18:42:59: 4000000 INFO @ Sun, 21 Jun 2020 18:43:03: 10000000 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 18:43:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2618521/SRX2618521.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2618521/SRX2618521.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2618521/SRX2618521.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2618521/SRX2618521.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 18:43:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:43:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:43:05: 5000000 INFO @ Sun, 21 Jun 2020 18:43:09: 11000000 INFO @ Sun, 21 Jun 2020 18:43:11: 1000000 INFO @ Sun, 21 Jun 2020 18:43:12: 6000000 INFO @ Sun, 21 Jun 2020 18:43:16: 12000000 INFO @ Sun, 21 Jun 2020 18:43:17: 2000000 INFO @ Sun, 21 Jun 2020 18:43:18: 7000000 INFO @ Sun, 21 Jun 2020 18:43:21: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:43:21: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:43:21: #1 total tags in treatment: 12686407 INFO @ Sun, 21 Jun 2020 18:43:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:43:21: #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 18:43:21: #1 tags after filtering in treatment: 12686404 INFO @ Sun, 21 Jun 2020 18:43:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:43:21: #1 finished! INFO @ Sun, 21 Jun 2020 18:43:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:43:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:43:22: #2 number of paired peaks: 669 WARNING @ Sun, 21 Jun 2020 18:43:22: Fewer paired peaks (669) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 669 pairs to build model! INFO @ Sun, 21 Jun 2020 18:43:22: start model_add_line... INFO @ Sun, 21 Jun 2020 18:43:22: start X-correlation... INFO @ Sun, 21 Jun 2020 18:43:22: end of X-cor INFO @ Sun, 21 Jun 2020 18:43:22: #2 finished! INFO @ Sun, 21 Jun 2020 18:43:22: #2 predicted fragment length is 76 bps INFO @ Sun, 21 Jun 2020 18:43:22: #2 alternative fragment length(s) may be 76 bps INFO @ Sun, 21 Jun 2020 18:43:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618521/SRX2618521.05_model.r WARNING @ Sun, 21 Jun 2020 18:43:22: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:43:22: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Sun, 21 Jun 2020 18:43:22: #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 18:43:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:43:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:43:23: 3000000 INFO @ Sun, 21 Jun 2020 18:43:24: 8000000 INFO @ Sun, 21 Jun 2020 18:43:29: 4000000 INFO @ Sun, 21 Jun 2020 18:43:31: 9000000 INFO @ Sun, 21 Jun 2020 18:43:35: 5000000 INFO @ Sun, 21 Jun 2020 18:43:37: 10000000 INFO @ Sun, 21 Jun 2020 18:43:42: 6000000 INFO @ Sun, 21 Jun 2020 18:43:44: 11000000 INFO @ Sun, 21 Jun 2020 18:43:48: 7000000 INFO @ Sun, 21 Jun 2020 18:43:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:43:50: 12000000 INFO @ Sun, 21 Jun 2020 18:43:54: 8000000 INFO @ Sun, 21 Jun 2020 18:43:55: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:43:55: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:43:55: #1 total tags in treatment: 12686407 INFO @ Sun, 21 Jun 2020 18:43:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:43:55: #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 18:43:55: #1 tags after filtering in treatment: 12686404 INFO @ Sun, 21 Jun 2020 18:43:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:43:55: #1 finished! INFO @ Sun, 21 Jun 2020 18:43:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:43:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:43:56: #2 number of paired peaks: 669 WARNING @ Sun, 21 Jun 2020 18:43:56: Fewer paired peaks (669) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 669 pairs to build model! INFO @ Sun, 21 Jun 2020 18:43:56: start model_add_line... INFO @ Sun, 21 Jun 2020 18:43:56: start X-correlation... INFO @ Sun, 21 Jun 2020 18:43:56: end of X-cor INFO @ Sun, 21 Jun 2020 18:43:56: #2 finished! INFO @ Sun, 21 Jun 2020 18:43:56: #2 predicted fragment length is 76 bps INFO @ Sun, 21 Jun 2020 18:43:56: #2 alternative fragment length(s) may be 76 bps INFO @ Sun, 21 Jun 2020 18:43:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618521/SRX2618521.10_model.r WARNING @ Sun, 21 Jun 2020 18:43:56: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:43:56: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Sun, 21 Jun 2020 18:43:56: #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 18:43:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:43:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:44:00: 9000000 INFO @ Sun, 21 Jun 2020 18:44:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618521/SRX2618521.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:44:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618521/SRX2618521.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:44:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618521/SRX2618521.05_summits.bed INFO @ Sun, 21 Jun 2020 18:44:01: Done! pass1 - making usageList (598 chroms): 2 millis pass2 - checking and writing primary data (6561 records, 4 fields): 21 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:44:06: 10000000 INFO @ Sun, 21 Jun 2020 18:44:12: 11000000 INFO @ Sun, 21 Jun 2020 18:44:18: 12000000 INFO @ Sun, 21 Jun 2020 18:44:22: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:44:22: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:44:22: #1 total tags in treatment: 12686407 INFO @ Sun, 21 Jun 2020 18:44:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:44:22: #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 18:44:22: #1 tags after filtering in treatment: 12686404 INFO @ Sun, 21 Jun 2020 18:44:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:44:22: #1 finished! INFO @ Sun, 21 Jun 2020 18:44:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:44:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:44:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:44:23: #2 number of paired peaks: 669 WARNING @ Sun, 21 Jun 2020 18:44:23: Fewer paired peaks (669) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 669 pairs to build model! INFO @ Sun, 21 Jun 2020 18:44:23: start model_add_line... INFO @ Sun, 21 Jun 2020 18:44:23: start X-correlation... INFO @ Sun, 21 Jun 2020 18:44:23: end of X-cor INFO @ Sun, 21 Jun 2020 18:44:23: #2 finished! INFO @ Sun, 21 Jun 2020 18:44:23: #2 predicted fragment length is 76 bps INFO @ Sun, 21 Jun 2020 18:44:23: #2 alternative fragment length(s) may be 76 bps INFO @ Sun, 21 Jun 2020 18:44:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2618521/SRX2618521.20_model.r WARNING @ Sun, 21 Jun 2020 18:44:23: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:44:23: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Sun, 21 Jun 2020 18:44:23: #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 18:44:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:44:23: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:44:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618521/SRX2618521.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:44:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618521/SRX2618521.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:44:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618521/SRX2618521.10_summits.bed INFO @ Sun, 21 Jun 2020 18:44:35: Done! pass1 - making usageList (509 chroms): 1 millis pass2 - checking and writing primary data (4086 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:44:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:45:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2618521/SRX2618521.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:45:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2618521/SRX2618521.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:45:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2618521/SRX2618521.20_summits.bed INFO @ Sun, 21 Jun 2020 18:45:01: Done! pass1 - making usageList (362 chroms): 1 millis pass2 - checking and writing primary data (1639 records, 4 fields): 12 millis CompletedMACS2peakCalling