Job ID = 6459315 SRX = SRX6685750 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:01:16 prefetch.2.10.7: 1) Downloading 'SRR9937043'... 2020-06-21T13:01:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:11:41 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:11:41 prefetch.2.10.7: 1) 'SRR9937043' was downloaded successfully 2020-06-21T13:11:41 prefetch.2.10.7: 'SRR9937043' has 0 unresolved dependencies Read 49577528 spots for SRR9937043/SRR9937043.sra Written 49577528 spots for SRR9937043/SRR9937043.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: 00:17:22 49577528 reads; of these: 49577528 (100.00%) were unpaired; of these: 11706610 (23.61%) aligned 0 times 25749481 (51.94%) aligned exactly 1 time 12121437 (24.45%) aligned >1 times 76.39% overall alignment rate Time searching: 00:17:22 Overall time: 00:17:22 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 16 files... [bam_rmdupse_core] 15674729 / 37870918 = 0.4139 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 22:42:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6685750/SRX6685750.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6685750/SRX6685750.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6685750/SRX6685750.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6685750/SRX6685750.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 22:42:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:42:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:43:04: 1000000 INFO @ Sun, 21 Jun 2020 22:43:10: 2000000 INFO @ Sun, 21 Jun 2020 22:43:15: 3000000 INFO @ Sun, 21 Jun 2020 22:43:21: 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 22:43:27: 5000000 INFO @ Sun, 21 Jun 2020 22:43:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6685750/SRX6685750.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6685750/SRX6685750.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6685750/SRX6685750.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6685750/SRX6685750.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 22:43:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:43:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:43:33: 6000000 INFO @ Sun, 21 Jun 2020 22:43:35: 1000000 INFO @ Sun, 21 Jun 2020 22:43:40: 7000000 INFO @ Sun, 21 Jun 2020 22:43:42: 2000000 INFO @ Sun, 21 Jun 2020 22:43:46: 8000000 INFO @ Sun, 21 Jun 2020 22:43:48: 3000000 INFO @ Sun, 21 Jun 2020 22:43:53: 9000000 INFO @ Sun, 21 Jun 2020 22:43:55: 4000000 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 22:43:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6685750/SRX6685750.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6685750/SRX6685750.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6685750/SRX6685750.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6685750/SRX6685750.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 22:43:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:43:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:43:59: 10000000 INFO @ Sun, 21 Jun 2020 22:44:01: 5000000 INFO @ Sun, 21 Jun 2020 22:44:05: 1000000 INFO @ Sun, 21 Jun 2020 22:44:06: 11000000 INFO @ Sun, 21 Jun 2020 22:44:08: 6000000 INFO @ Sun, 21 Jun 2020 22:44:12: 2000000 INFO @ Sun, 21 Jun 2020 22:44:13: 12000000 INFO @ Sun, 21 Jun 2020 22:44:15: 7000000 INFO @ Sun, 21 Jun 2020 22:44:18: 3000000 INFO @ Sun, 21 Jun 2020 22:44:20: 13000000 INFO @ Sun, 21 Jun 2020 22:44:22: 8000000 INFO @ Sun, 21 Jun 2020 22:44:25: 4000000 INFO @ Sun, 21 Jun 2020 22:44:26: 14000000 INFO @ Sun, 21 Jun 2020 22:44:28: 9000000 INFO @ Sun, 21 Jun 2020 22:44:32: 5000000 INFO @ Sun, 21 Jun 2020 22:44:33: 15000000 INFO @ Sun, 21 Jun 2020 22:44:35: 10000000 INFO @ Sun, 21 Jun 2020 22:44:38: 6000000 INFO @ Sun, 21 Jun 2020 22:44:39: 16000000 INFO @ Sun, 21 Jun 2020 22:44:41: 11000000 INFO @ Sun, 21 Jun 2020 22:44:45: 7000000 INFO @ Sun, 21 Jun 2020 22:44:46: 17000000 INFO @ Sun, 21 Jun 2020 22:44:48: 12000000 INFO @ Sun, 21 Jun 2020 22:44:52: 8000000 INFO @ Sun, 21 Jun 2020 22:44:52: 18000000 INFO @ Sun, 21 Jun 2020 22:44:55: 13000000 INFO @ Sun, 21 Jun 2020 22:44:58: 9000000 INFO @ Sun, 21 Jun 2020 22:44:59: 19000000 INFO @ Sun, 21 Jun 2020 22:45:01: 14000000 INFO @ Sun, 21 Jun 2020 22:45:05: 10000000 INFO @ Sun, 21 Jun 2020 22:45:06: 20000000 INFO @ Sun, 21 Jun 2020 22:45:08: 15000000 INFO @ Sun, 21 Jun 2020 22:45:12: 11000000 INFO @ Sun, 21 Jun 2020 22:45:12: 21000000 INFO @ Sun, 21 Jun 2020 22:45:14: 16000000 INFO @ Sun, 21 Jun 2020 22:45:18: 12000000 INFO @ Sun, 21 Jun 2020 22:45:19: 22000000 INFO @ Sun, 21 Jun 2020 22:45:21: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 22:45:21: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 22:45:21: #1 total tags in treatment: 22196189 INFO @ Sun, 21 Jun 2020 22:45:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:45:21: #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 22:45:21: 17000000 INFO @ Sun, 21 Jun 2020 22:45:21: #1 tags after filtering in treatment: 22196106 INFO @ Sun, 21 Jun 2020 22:45:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:45:21: #1 finished! INFO @ Sun, 21 Jun 2020 22:45:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:45:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:45:23: #2 number of paired peaks: 2332 INFO @ Sun, 21 Jun 2020 22:45:23: start model_add_line... INFO @ Sun, 21 Jun 2020 22:45:23: start X-correlation... INFO @ Sun, 21 Jun 2020 22:45:23: end of X-cor INFO @ Sun, 21 Jun 2020 22:45:23: #2 finished! INFO @ Sun, 21 Jun 2020 22:45:23: #2 predicted fragment length is 77 bps INFO @ Sun, 21 Jun 2020 22:45:23: #2 alternative fragment length(s) may be 2,77 bps INFO @ Sun, 21 Jun 2020 22:45:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6685750/SRX6685750.05_model.r WARNING @ Sun, 21 Jun 2020 22:45:23: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:45:23: #2 You may need to consider one of the other alternative d(s): 2,77 WARNING @ Sun, 21 Jun 2020 22:45:23: #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 22:45:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:45:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:45:25: 13000000 INFO @ Sun, 21 Jun 2020 22:45:27: 18000000 INFO @ Sun, 21 Jun 2020 22:45:31: 14000000 INFO @ Sun, 21 Jun 2020 22:45:34: 19000000 INFO @ Sun, 21 Jun 2020 22:45:38: 15000000 INFO @ Sun, 21 Jun 2020 22:45:41: 20000000 INFO @ Sun, 21 Jun 2020 22:45:44: 16000000 INFO @ Sun, 21 Jun 2020 22:45:47: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:45:51: 17000000 INFO @ Sun, 21 Jun 2020 22:45:54: 22000000 INFO @ Sun, 21 Jun 2020 22:45:55: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 22:45:55: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 22:45:55: #1 total tags in treatment: 22196189 INFO @ Sun, 21 Jun 2020 22:45:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:45:55: #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 22:45:56: #1 tags after filtering in treatment: 22196106 INFO @ Sun, 21 Jun 2020 22:45:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:45:56: #1 finished! INFO @ Sun, 21 Jun 2020 22:45:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:45:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:45:57: 18000000 INFO @ Sun, 21 Jun 2020 22:45:58: #2 number of paired peaks: 2332 INFO @ Sun, 21 Jun 2020 22:45:58: start model_add_line... INFO @ Sun, 21 Jun 2020 22:45:58: start X-correlation... INFO @ Sun, 21 Jun 2020 22:45:58: end of X-cor INFO @ Sun, 21 Jun 2020 22:45:58: #2 finished! INFO @ Sun, 21 Jun 2020 22:45:58: #2 predicted fragment length is 77 bps INFO @ Sun, 21 Jun 2020 22:45:58: #2 alternative fragment length(s) may be 2,77 bps INFO @ Sun, 21 Jun 2020 22:45:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6685750/SRX6685750.10_model.r WARNING @ Sun, 21 Jun 2020 22:45:58: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:45:58: #2 You may need to consider one of the other alternative d(s): 2,77 WARNING @ Sun, 21 Jun 2020 22:45:58: #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 22:45:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:45:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:46:04: 19000000 INFO @ Sun, 21 Jun 2020 22:46:09: 20000000 INFO @ Sun, 21 Jun 2020 22:46:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:46:15: 21000000 INFO @ Sun, 21 Jun 2020 22:46:21: 22000000 INFO @ Sun, 21 Jun 2020 22:46:23: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 22:46:23: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 22:46:23: #1 total tags in treatment: 22196189 INFO @ Sun, 21 Jun 2020 22:46:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:46:23: #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 22:46:23: #1 tags after filtering in treatment: 22196106 INFO @ Sun, 21 Jun 2020 22:46:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:46:23: #1 finished! INFO @ Sun, 21 Jun 2020 22:46:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:46:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:46:25: #2 number of paired peaks: 2332 INFO @ Sun, 21 Jun 2020 22:46:25: start model_add_line... INFO @ Sun, 21 Jun 2020 22:46:25: start X-correlation... INFO @ Sun, 21 Jun 2020 22:46:25: end of X-cor INFO @ Sun, 21 Jun 2020 22:46:25: #2 finished! INFO @ Sun, 21 Jun 2020 22:46:25: #2 predicted fragment length is 77 bps INFO @ Sun, 21 Jun 2020 22:46:25: #2 alternative fragment length(s) may be 2,77 bps INFO @ Sun, 21 Jun 2020 22:46:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6685750/SRX6685750.20_model.r WARNING @ Sun, 21 Jun 2020 22:46:25: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:46:25: #2 You may need to consider one of the other alternative d(s): 2,77 WARNING @ Sun, 21 Jun 2020 22:46:25: #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 22:46:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:46:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:46:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6685750/SRX6685750.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:46:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6685750/SRX6685750.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:46:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6685750/SRX6685750.05_summits.bed INFO @ Sun, 21 Jun 2020 22:46:35: Done! pass1 - making usageList (773 chroms): 2 millis pass2 - checking and writing primary data (4818 records, 4 fields): 26 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:46:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:47:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6685750/SRX6685750.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:47:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6685750/SRX6685750.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:47:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6685750/SRX6685750.10_summits.bed INFO @ Sun, 21 Jun 2020 22:47:07: Done! pass1 - making usageList (678 chroms): 1 millis pass2 - checking and writing primary data (2907 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:47:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:47:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6685750/SRX6685750.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:47:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6685750/SRX6685750.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:47:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6685750/SRX6685750.20_summits.bed INFO @ Sun, 21 Jun 2020 22:47:34: Done! pass1 - making usageList (540 chroms): 1 millis pass2 - checking and writing primary data (1842 records, 4 fields): 18 millis CompletedMACS2peakCalling