Job ID = 6459309 SRX = SRX6685744 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:18:01 prefetch.2.10.7: 1) Downloading 'SRR9937037'... 2020-06-21T13:18:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:25:33 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:25:33 prefetch.2.10.7: 1) 'SRR9937037' was downloaded successfully 2020-06-21T13:25:33 prefetch.2.10.7: 'SRR9937037' has 0 unresolved dependencies Read 50844759 spots for SRR9937037/SRR9937037.sra Written 50844759 spots for SRR9937037/SRR9937037.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: 00:16:43 50844759 reads; of these: 50844759 (100.00%) were unpaired; of these: 4716444 (9.28%) aligned 0 times 35676640 (70.17%) aligned exactly 1 time 10451675 (20.56%) aligned >1 times 90.72% overall alignment rate Time searching: 00:16:43 Overall time: 00:16:43 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 20 files... [bam_rmdupse_core] 22691410 / 46128315 = 0.4919 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 22:56:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6685744/SRX6685744.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6685744/SRX6685744.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6685744/SRX6685744.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6685744/SRX6685744.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 22:56:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:56:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:56:44: 1000000 INFO @ Sun, 21 Jun 2020 22:56:51: 2000000 INFO @ Sun, 21 Jun 2020 22:56:58: 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 22:57:06: 4000000 INFO @ Sun, 21 Jun 2020 22:57:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6685744/SRX6685744.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6685744/SRX6685744.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6685744/SRX6685744.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6685744/SRX6685744.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 22:57:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:57:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:57:13: 5000000 INFO @ Sun, 21 Jun 2020 22:57:15: 1000000 INFO @ Sun, 21 Jun 2020 22:57:21: 6000000 INFO @ Sun, 21 Jun 2020 22:57:23: 2000000 INFO @ Sun, 21 Jun 2020 22:57:29: 7000000 INFO @ Sun, 21 Jun 2020 22:57:31: 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 @ Sun, 21 Jun 2020 22:57:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6685744/SRX6685744.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6685744/SRX6685744.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6685744/SRX6685744.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6685744/SRX6685744.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 22:57:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:57:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:57:37: 8000000 INFO @ Sun, 21 Jun 2020 22:57:40: 4000000 INFO @ Sun, 21 Jun 2020 22:57:45: 9000000 INFO @ Sun, 21 Jun 2020 22:57:45: 1000000 INFO @ Sun, 21 Jun 2020 22:57:48: 5000000 INFO @ Sun, 21 Jun 2020 22:57:53: 10000000 INFO @ Sun, 21 Jun 2020 22:57:53: 2000000 INFO @ Sun, 21 Jun 2020 22:57:56: 6000000 INFO @ Sun, 21 Jun 2020 22:58:01: 11000000 INFO @ Sun, 21 Jun 2020 22:58:02: 3000000 INFO @ Sun, 21 Jun 2020 22:58:05: 7000000 INFO @ Sun, 21 Jun 2020 22:58:09: 12000000 INFO @ Sun, 21 Jun 2020 22:58:10: 4000000 INFO @ Sun, 21 Jun 2020 22:58:14: 8000000 INFO @ Sun, 21 Jun 2020 22:58:17: 13000000 INFO @ Sun, 21 Jun 2020 22:58:18: 5000000 INFO @ Sun, 21 Jun 2020 22:58:22: 9000000 INFO @ Sun, 21 Jun 2020 22:58:25: 14000000 INFO @ Sun, 21 Jun 2020 22:58:26: 6000000 INFO @ Sun, 21 Jun 2020 22:58:31: 10000000 INFO @ Sun, 21 Jun 2020 22:58:33: 15000000 INFO @ Sun, 21 Jun 2020 22:58:34: 7000000 INFO @ Sun, 21 Jun 2020 22:58:39: 11000000 INFO @ Sun, 21 Jun 2020 22:58:41: 16000000 INFO @ Sun, 21 Jun 2020 22:58:42: 8000000 INFO @ Sun, 21 Jun 2020 22:58:48: 12000000 INFO @ Sun, 21 Jun 2020 22:58:49: 17000000 INFO @ Sun, 21 Jun 2020 22:58:50: 9000000 INFO @ Sun, 21 Jun 2020 22:58:57: 13000000 INFO @ Sun, 21 Jun 2020 22:58:57: 18000000 INFO @ Sun, 21 Jun 2020 22:58:58: 10000000 INFO @ Sun, 21 Jun 2020 22:59:05: 19000000 INFO @ Sun, 21 Jun 2020 22:59:06: 14000000 INFO @ Sun, 21 Jun 2020 22:59:07: 11000000 INFO @ Sun, 21 Jun 2020 22:59:15: 20000000 INFO @ Sun, 21 Jun 2020 22:59:15: 15000000 INFO @ Sun, 21 Jun 2020 22:59:15: 12000000 INFO @ Sun, 21 Jun 2020 22:59:23: 21000000 INFO @ Sun, 21 Jun 2020 22:59:24: 16000000 INFO @ Sun, 21 Jun 2020 22:59:24: 13000000 INFO @ Sun, 21 Jun 2020 22:59:32: 22000000 INFO @ Sun, 21 Jun 2020 22:59:32: 17000000 INFO @ Sun, 21 Jun 2020 22:59:33: 14000000 INFO @ Sun, 21 Jun 2020 22:59:40: 23000000 INFO @ Sun, 21 Jun 2020 22:59:41: 18000000 INFO @ Sun, 21 Jun 2020 22:59:41: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:59:44: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 22:59:44: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 22:59:44: #1 total tags in treatment: 23436905 INFO @ Sun, 21 Jun 2020 22:59:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:59:44: #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 22:59:45: #1 tags after filtering in treatment: 23436839 INFO @ Sun, 21 Jun 2020 22:59:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:59:45: #1 finished! INFO @ Sun, 21 Jun 2020 22:59:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:59:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:59:47: #2 number of paired peaks: 2621 INFO @ Sun, 21 Jun 2020 22:59:47: start model_add_line... INFO @ Sun, 21 Jun 2020 22:59:47: start X-correlation... INFO @ Sun, 21 Jun 2020 22:59:47: end of X-cor INFO @ Sun, 21 Jun 2020 22:59:47: #2 finished! INFO @ Sun, 21 Jun 2020 22:59:47: #2 predicted fragment length is 123 bps INFO @ Sun, 21 Jun 2020 22:59:47: #2 alternative fragment length(s) may be 123 bps INFO @ Sun, 21 Jun 2020 22:59:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6685744/SRX6685744.05_model.r WARNING @ Sun, 21 Jun 2020 22:59:47: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:59:47: #2 You may need to consider one of the other alternative d(s): 123 WARNING @ Sun, 21 Jun 2020 22:59:47: #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 22:59:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:59:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:59:49: 19000000 INFO @ Sun, 21 Jun 2020 22:59:50: 16000000 INFO @ Sun, 21 Jun 2020 22:59:57: 20000000 INFO @ Sun, 21 Jun 2020 22:59:58: 17000000 INFO @ Sun, 21 Jun 2020 23:00:06: 21000000 INFO @ Sun, 21 Jun 2020 23:00:06: 18000000 INFO @ Sun, 21 Jun 2020 23:00:14: 22000000 INFO @ Sun, 21 Jun 2020 23:00:14: 19000000 INFO @ Sun, 21 Jun 2020 23:00:22: 23000000 INFO @ Sun, 21 Jun 2020 23:00:23: 20000000 INFO @ Sun, 21 Jun 2020 23:00:26: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 23:00:26: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 23:00:26: #1 total tags in treatment: 23436905 INFO @ Sun, 21 Jun 2020 23:00:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 23:00:26: #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 23:00:26: #1 tags after filtering in treatment: 23436839 INFO @ Sun, 21 Jun 2020 23:00:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 23:00:26: #1 finished! INFO @ Sun, 21 Jun 2020 23:00:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 23:00:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 23:00:28: #2 number of paired peaks: 2621 INFO @ Sun, 21 Jun 2020 23:00:28: start model_add_line... INFO @ Sun, 21 Jun 2020 23:00:28: start X-correlation... INFO @ Sun, 21 Jun 2020 23:00:28: end of X-cor INFO @ Sun, 21 Jun 2020 23:00:28: #2 finished! INFO @ Sun, 21 Jun 2020 23:00:28: #2 predicted fragment length is 123 bps INFO @ Sun, 21 Jun 2020 23:00:28: #2 alternative fragment length(s) may be 123 bps INFO @ Sun, 21 Jun 2020 23:00:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6685744/SRX6685744.10_model.r WARNING @ Sun, 21 Jun 2020 23:00:28: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 23:00:28: #2 You may need to consider one of the other alternative d(s): 123 WARNING @ Sun, 21 Jun 2020 23:00:28: #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 23:00:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 23:00:28: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 23:00:31: 21000000 INFO @ Sun, 21 Jun 2020 23:00:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 23:00:38: 22000000 INFO @ Sun, 21 Jun 2020 23:00:45: 23000000 INFO @ Sun, 21 Jun 2020 23:00:49: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 23:00:49: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 23:00:49: #1 total tags in treatment: 23436905 INFO @ Sun, 21 Jun 2020 23:00:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 23:00:49: #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 23:00:50: #1 tags after filtering in treatment: 23436839 INFO @ Sun, 21 Jun 2020 23:00:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 23:00:50: #1 finished! INFO @ Sun, 21 Jun 2020 23:00:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 23:00:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 23:00:51: #2 number of paired peaks: 2621 INFO @ Sun, 21 Jun 2020 23:00:51: start model_add_line... INFO @ Sun, 21 Jun 2020 23:00:52: start X-correlation... INFO @ Sun, 21 Jun 2020 23:00:52: end of X-cor INFO @ Sun, 21 Jun 2020 23:00:52: #2 finished! INFO @ Sun, 21 Jun 2020 23:00:52: #2 predicted fragment length is 123 bps INFO @ Sun, 21 Jun 2020 23:00:52: #2 alternative fragment length(s) may be 123 bps INFO @ Sun, 21 Jun 2020 23:00:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6685744/SRX6685744.20_model.r WARNING @ Sun, 21 Jun 2020 23:00:52: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 23:00:52: #2 You may need to consider one of the other alternative d(s): 123 WARNING @ Sun, 21 Jun 2020 23:00:52: #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 23:00:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 23:00:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 23:01:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6685744/SRX6685744.05_peaks.xls INFO @ Sun, 21 Jun 2020 23:01:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6685744/SRX6685744.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:01:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6685744/SRX6685744.05_summits.bed INFO @ Sun, 21 Jun 2020 23:01:02: Done! pass1 - making usageList (707 chroms): 3 millis pass2 - checking and writing primary data (16830 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 23:01:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 23:01:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 23:01:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6685744/SRX6685744.10_peaks.xls INFO @ Sun, 21 Jun 2020 23:01:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6685744/SRX6685744.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:01:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6685744/SRX6685744.10_summits.bed INFO @ Sun, 21 Jun 2020 23:01:42: Done! pass1 - making usageList (641 chroms): 3 millis pass2 - checking and writing primary data (14005 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 23:02:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6685744/SRX6685744.20_peaks.xls INFO @ Sun, 21 Jun 2020 23:02:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6685744/SRX6685744.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:02:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6685744/SRX6685744.20_summits.bed INFO @ Sun, 21 Jun 2020 23:02:06: Done! pass1 - making usageList (556 chroms): 2 millis pass2 - checking and writing primary data (10856 records, 4 fields): 24 millis CompletedMACS2peakCalling