Job ID = 6459312 SRX = SRX6685747 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:02:49 prefetch.2.10.7: 1) Downloading 'SRR9937040'... 2020-06-21T13:02:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:07:51 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:07:51 prefetch.2.10.7: 1) 'SRR9937040' was downloaded successfully 2020-06-21T13:07:51 prefetch.2.10.7: 'SRR9937040' has 0 unresolved dependencies Read 34208103 spots for SRR9937040/SRR9937040.sra Written 34208103 spots for SRR9937040/SRR9937040.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: 00:11:57 34208103 reads; of these: 34208103 (100.00%) were unpaired; of these: 5226004 (15.28%) aligned 0 times 20438804 (59.75%) aligned exactly 1 time 8543295 (24.97%) aligned >1 times 84.72% overall alignment rate Time searching: 00:11:57 Overall time: 00:11:57 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 12 files... [bam_rmdupse_core] 8396023 / 28982099 = 0.2897 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 22:31:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6685747/SRX6685747.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6685747/SRX6685747.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6685747/SRX6685747.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6685747/SRX6685747.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 22:31:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:31:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:31:12: 1000000 INFO @ Sun, 21 Jun 2020 22:31:18: 2000000 INFO @ Sun, 21 Jun 2020 22:31:24: 3000000 INFO @ Sun, 21 Jun 2020 22:31:30: 4000000 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 22:31:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6685747/SRX6685747.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6685747/SRX6685747.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6685747/SRX6685747.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6685747/SRX6685747.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 22:31:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:31:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:31:37: 5000000 INFO @ Sun, 21 Jun 2020 22:31:43: 1000000 INFO @ Sun, 21 Jun 2020 22:31:44: 6000000 INFO @ Sun, 21 Jun 2020 22:31:50: 2000000 INFO @ Sun, 21 Jun 2020 22:31:51: 7000000 INFO @ Sun, 21 Jun 2020 22:31:57: 3000000 INFO @ Sun, 21 Jun 2020 22:31:59: 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 22:32:05: 4000000 INFO @ Sun, 21 Jun 2020 22:32:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6685747/SRX6685747.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6685747/SRX6685747.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6685747/SRX6685747.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6685747/SRX6685747.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 22:32:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:32:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:32:06: 9000000 INFO @ Sun, 21 Jun 2020 22:32:13: 5000000 INFO @ Sun, 21 Jun 2020 22:32:14: 10000000 INFO @ Sun, 21 Jun 2020 22:32:14: 1000000 INFO @ Sun, 21 Jun 2020 22:32:21: 6000000 INFO @ Sun, 21 Jun 2020 22:32:22: 11000000 INFO @ Sun, 21 Jun 2020 22:32:23: 2000000 INFO @ Sun, 21 Jun 2020 22:32:28: 7000000 INFO @ Sun, 21 Jun 2020 22:32:30: 12000000 INFO @ Sun, 21 Jun 2020 22:32:31: 3000000 INFO @ Sun, 21 Jun 2020 22:32:36: 8000000 INFO @ Sun, 21 Jun 2020 22:32:37: 13000000 INFO @ Sun, 21 Jun 2020 22:32:40: 4000000 INFO @ Sun, 21 Jun 2020 22:32:44: 9000000 INFO @ Sun, 21 Jun 2020 22:32:45: 14000000 INFO @ Sun, 21 Jun 2020 22:32:49: 5000000 INFO @ Sun, 21 Jun 2020 22:32:52: 10000000 INFO @ Sun, 21 Jun 2020 22:32:53: 15000000 INFO @ Sun, 21 Jun 2020 22:32:58: 6000000 INFO @ Sun, 21 Jun 2020 22:33:00: 11000000 INFO @ Sun, 21 Jun 2020 22:33:00: 16000000 INFO @ Sun, 21 Jun 2020 22:33:07: 7000000 INFO @ Sun, 21 Jun 2020 22:33:08: 12000000 INFO @ Sun, 21 Jun 2020 22:33:08: 17000000 INFO @ Sun, 21 Jun 2020 22:33:16: 8000000 INFO @ Sun, 21 Jun 2020 22:33:16: 13000000 INFO @ Sun, 21 Jun 2020 22:33:16: 18000000 INFO @ Sun, 21 Jun 2020 22:33:23: 14000000 INFO @ Sun, 21 Jun 2020 22:33:24: 19000000 INFO @ Sun, 21 Jun 2020 22:33:24: 9000000 INFO @ Sun, 21 Jun 2020 22:33:31: 15000000 INFO @ Sun, 21 Jun 2020 22:33:32: 20000000 INFO @ Sun, 21 Jun 2020 22:33:33: 10000000 INFO @ Sun, 21 Jun 2020 22:33:37: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 22:33:37: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 22:33:37: #1 total tags in treatment: 20586076 INFO @ Sun, 21 Jun 2020 22:33:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:33:37: #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 22:33:37: #1 tags after filtering in treatment: 20586001 INFO @ Sun, 21 Jun 2020 22:33:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:33:37: #1 finished! INFO @ Sun, 21 Jun 2020 22:33:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:33:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:33:39: #2 number of paired peaks: 1987 INFO @ Sun, 21 Jun 2020 22:33:39: start model_add_line... INFO @ Sun, 21 Jun 2020 22:33:39: 16000000 INFO @ Sun, 21 Jun 2020 22:33:39: start X-correlation... INFO @ Sun, 21 Jun 2020 22:33:39: end of X-cor INFO @ Sun, 21 Jun 2020 22:33:39: #2 finished! INFO @ Sun, 21 Jun 2020 22:33:39: #2 predicted fragment length is 121 bps INFO @ Sun, 21 Jun 2020 22:33:39: #2 alternative fragment length(s) may be 121 bps INFO @ Sun, 21 Jun 2020 22:33:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6685747/SRX6685747.05_model.r WARNING @ Sun, 21 Jun 2020 22:33:39: #2 Since the d (121) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:33:39: #2 You may need to consider one of the other alternative d(s): 121 WARNING @ Sun, 21 Jun 2020 22:33:39: #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 22:33:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:33:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:33:42: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:33:47: 17000000 INFO @ Sun, 21 Jun 2020 22:33:50: 12000000 INFO @ Sun, 21 Jun 2020 22:33:55: 18000000 INFO @ Sun, 21 Jun 2020 22:33:59: 13000000 INFO @ Sun, 21 Jun 2020 22:34:03: 19000000 INFO @ Sun, 21 Jun 2020 22:34:07: 14000000 INFO @ Sun, 21 Jun 2020 22:34:11: 20000000 INFO @ Sun, 21 Jun 2020 22:34:15: 15000000 INFO @ Sun, 21 Jun 2020 22:34:16: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 22:34:16: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 22:34:16: #1 total tags in treatment: 20586076 INFO @ Sun, 21 Jun 2020 22:34:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:34:16: #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 22:34:16: #1 tags after filtering in treatment: 20586001 INFO @ Sun, 21 Jun 2020 22:34:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:34:16: #1 finished! INFO @ Sun, 21 Jun 2020 22:34:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:34:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:34:18: #2 number of paired peaks: 1987 INFO @ Sun, 21 Jun 2020 22:34:18: start model_add_line... INFO @ Sun, 21 Jun 2020 22:34:18: start X-correlation... INFO @ Sun, 21 Jun 2020 22:34:18: end of X-cor INFO @ Sun, 21 Jun 2020 22:34:18: #2 finished! INFO @ Sun, 21 Jun 2020 22:34:18: #2 predicted fragment length is 121 bps INFO @ Sun, 21 Jun 2020 22:34:18: #2 alternative fragment length(s) may be 121 bps INFO @ Sun, 21 Jun 2020 22:34:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6685747/SRX6685747.10_model.r WARNING @ Sun, 21 Jun 2020 22:34:18: #2 Since the d (121) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:34:18: #2 You may need to consider one of the other alternative d(s): 121 WARNING @ Sun, 21 Jun 2020 22:34:18: #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 22:34:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:34:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:34:21: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:34:23: 16000000 INFO @ Sun, 21 Jun 2020 22:34:31: 17000000 INFO @ Sun, 21 Jun 2020 22:34:39: 18000000 INFO @ Sun, 21 Jun 2020 22:34:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6685747/SRX6685747.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:34:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6685747/SRX6685747.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:34:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6685747/SRX6685747.05_summits.bed INFO @ Sun, 21 Jun 2020 22:34:43: Done! pass1 - making usageList (718 chroms): 2 millis pass2 - checking and writing primary data (8750 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:34:47: 19000000 INFO @ Sun, 21 Jun 2020 22:34:55: 20000000 INFO @ Sun, 21 Jun 2020 22:34:59: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 22:34:59: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 22:34:59: #1 total tags in treatment: 20586076 INFO @ Sun, 21 Jun 2020 22:34:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:34:59: #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 22:35:00: #1 tags after filtering in treatment: 20586001 INFO @ Sun, 21 Jun 2020 22:35:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:35:00: #1 finished! INFO @ Sun, 21 Jun 2020 22:35:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:35:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:35:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:35:01: #2 number of paired peaks: 1987 INFO @ Sun, 21 Jun 2020 22:35:01: start model_add_line... INFO @ Sun, 21 Jun 2020 22:35:02: start X-correlation... INFO @ Sun, 21 Jun 2020 22:35:02: end of X-cor INFO @ Sun, 21 Jun 2020 22:35:02: #2 finished! INFO @ Sun, 21 Jun 2020 22:35:02: #2 predicted fragment length is 121 bps INFO @ Sun, 21 Jun 2020 22:35:02: #2 alternative fragment length(s) may be 121 bps INFO @ Sun, 21 Jun 2020 22:35:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6685747/SRX6685747.20_model.r WARNING @ Sun, 21 Jun 2020 22:35:02: #2 Since the d (121) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:35:02: #2 You may need to consider one of the other alternative d(s): 121 WARNING @ Sun, 21 Jun 2020 22:35:02: #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 22:35:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:35:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:35:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6685747/SRX6685747.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:35:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6685747/SRX6685747.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:35:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6685747/SRX6685747.10_summits.bed INFO @ Sun, 21 Jun 2020 22:35:22: Done! pass1 - making usageList (628 chroms): 2 millis pass2 - checking and writing primary data (7037 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:35:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:36:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6685747/SRX6685747.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:36:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6685747/SRX6685747.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:36:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6685747/SRX6685747.20_summits.bed INFO @ Sun, 21 Jun 2020 22:36:03: Done! pass1 - making usageList (536 chroms): 1 millis pass2 - checking and writing primary data (5439 records, 4 fields): 20 millis CompletedMACS2peakCalling