Job ID = 6527805 SRX = SRX287685 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T14:07:51 prefetch.2.10.7: 1) Downloading 'SRR869873'... 2020-06-29T14:07:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:12:31 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:12:31 prefetch.2.10.7: 1) 'SRR869873' was downloaded successfully Read 26924228 spots for SRR869873/SRR869873.sra Written 26924228 spots for SRR869873/SRR869873.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:56 26924228 reads; of these: 26924228 (100.00%) were unpaired; of these: 1125844 (4.18%) aligned 0 times 17097027 (63.50%) aligned exactly 1 time 8701357 (32.32%) aligned >1 times 95.82% 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: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 3991273 / 25798384 = 0.1547 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 23:41:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287685/SRX287685.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287685/SRX287685.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287685/SRX287685.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287685/SRX287685.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 23:41:43: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:41:43: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:41:49: 1000000 INFO @ Mon, 29 Jun 2020 23:41:56: 2000000 INFO @ Mon, 29 Jun 2020 23:42:03: 3000000 INFO @ Mon, 29 Jun 2020 23:42:10: 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 @ Mon, 29 Jun 2020 23:42:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287685/SRX287685.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287685/SRX287685.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287685/SRX287685.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287685/SRX287685.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 23:42:13: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:42:13: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:42:17: 5000000 INFO @ Mon, 29 Jun 2020 23:42:20: 1000000 INFO @ Mon, 29 Jun 2020 23:42:25: 6000000 INFO @ Mon, 29 Jun 2020 23:42:28: 2000000 INFO @ Mon, 29 Jun 2020 23:42:32: 7000000 INFO @ Mon, 29 Jun 2020 23:42:35: 3000000 INFO @ Mon, 29 Jun 2020 23:42:39: 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 @ Mon, 29 Jun 2020 23:42:42: 4000000 INFO @ Mon, 29 Jun 2020 23:42:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287685/SRX287685.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287685/SRX287685.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287685/SRX287685.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287685/SRX287685.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 23:42:43: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:42:43: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:42:47: 9000000 INFO @ Mon, 29 Jun 2020 23:42:50: 5000000 INFO @ Mon, 29 Jun 2020 23:42:51: 1000000 INFO @ Mon, 29 Jun 2020 23:42:55: 10000000 INFO @ Mon, 29 Jun 2020 23:42:58: 6000000 INFO @ Mon, 29 Jun 2020 23:43:00: 2000000 INFO @ Mon, 29 Jun 2020 23:43:03: 11000000 INFO @ Mon, 29 Jun 2020 23:43:06: 7000000 INFO @ Mon, 29 Jun 2020 23:43:08: 3000000 INFO @ Mon, 29 Jun 2020 23:43:10: 12000000 INFO @ Mon, 29 Jun 2020 23:43:13: 8000000 INFO @ Mon, 29 Jun 2020 23:43:16: 4000000 INFO @ Mon, 29 Jun 2020 23:43:18: 13000000 INFO @ Mon, 29 Jun 2020 23:43:21: 9000000 INFO @ Mon, 29 Jun 2020 23:43:25: 5000000 INFO @ Mon, 29 Jun 2020 23:43:26: 14000000 INFO @ Mon, 29 Jun 2020 23:43:29: 10000000 INFO @ Mon, 29 Jun 2020 23:43:33: 6000000 INFO @ Mon, 29 Jun 2020 23:43:33: 15000000 INFO @ Mon, 29 Jun 2020 23:43:36: 11000000 INFO @ Mon, 29 Jun 2020 23:43:41: 16000000 INFO @ Mon, 29 Jun 2020 23:43:42: 7000000 INFO @ Mon, 29 Jun 2020 23:43:44: 12000000 INFO @ Mon, 29 Jun 2020 23:43:49: 17000000 INFO @ Mon, 29 Jun 2020 23:43:50: 8000000 INFO @ Mon, 29 Jun 2020 23:43:52: 13000000 INFO @ Mon, 29 Jun 2020 23:43:57: 18000000 INFO @ Mon, 29 Jun 2020 23:43:59: 9000000 INFO @ Mon, 29 Jun 2020 23:43:59: 14000000 INFO @ Mon, 29 Jun 2020 23:44:05: 19000000 INFO @ Mon, 29 Jun 2020 23:44:07: 15000000 INFO @ Mon, 29 Jun 2020 23:44:07: 10000000 INFO @ Mon, 29 Jun 2020 23:44:13: 20000000 INFO @ Mon, 29 Jun 2020 23:44:14: 16000000 INFO @ Mon, 29 Jun 2020 23:44:16: 11000000 INFO @ Mon, 29 Jun 2020 23:44:20: 21000000 INFO @ Mon, 29 Jun 2020 23:44:22: 17000000 INFO @ Mon, 29 Jun 2020 23:44:24: 12000000 INFO @ Mon, 29 Jun 2020 23:44:26: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:44:26: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:44:26: #1 total tags in treatment: 21807111 INFO @ Mon, 29 Jun 2020 23:44:26: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:44:26: #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 23:44:27: #1 tags after filtering in treatment: 21807111 INFO @ Mon, 29 Jun 2020 23:44:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:44:27: #1 finished! INFO @ Mon, 29 Jun 2020 23:44:27: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:44:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:44:28: #2 number of paired peaks: 171 WARNING @ Mon, 29 Jun 2020 23:44:28: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Mon, 29 Jun 2020 23:44:28: start model_add_line... INFO @ Mon, 29 Jun 2020 23:44:28: start X-correlation... INFO @ Mon, 29 Jun 2020 23:44:28: end of X-cor INFO @ Mon, 29 Jun 2020 23:44:28: #2 finished! INFO @ Mon, 29 Jun 2020 23:44:28: #2 predicted fragment length is 40 bps INFO @ Mon, 29 Jun 2020 23:44:28: #2 alternative fragment length(s) may be 40 bps INFO @ Mon, 29 Jun 2020 23:44:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287685/SRX287685.05_model.r WARNING @ Mon, 29 Jun 2020 23:44:28: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:44:28: #2 You may need to consider one of the other alternative d(s): 40 WARNING @ Mon, 29 Jun 2020 23:44:28: #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 23:44:28: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:44:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:44:29: 18000000 INFO @ Mon, 29 Jun 2020 23:44:32: 13000000 INFO @ Mon, 29 Jun 2020 23:44:36: 19000000 INFO @ Mon, 29 Jun 2020 23:44:41: 14000000 INFO @ Mon, 29 Jun 2020 23:44:43: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:44:49: 15000000 INFO @ Mon, 29 Jun 2020 23:44:50: 21000000 INFO @ Mon, 29 Jun 2020 23:44:56: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:44:56: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:44:56: #1 total tags in treatment: 21807111 INFO @ Mon, 29 Jun 2020 23:44:56: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:44:56: #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 23:44:57: #1 tags after filtering in treatment: 21807111 INFO @ Mon, 29 Jun 2020 23:44:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:44:57: #1 finished! INFO @ Mon, 29 Jun 2020 23:44:57: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:44:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:44:58: 16000000 INFO @ Mon, 29 Jun 2020 23:44:58: #2 number of paired peaks: 171 WARNING @ Mon, 29 Jun 2020 23:44:58: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Mon, 29 Jun 2020 23:44:58: start model_add_line... INFO @ Mon, 29 Jun 2020 23:44:58: start X-correlation... INFO @ Mon, 29 Jun 2020 23:44:58: end of X-cor INFO @ Mon, 29 Jun 2020 23:44:58: #2 finished! INFO @ Mon, 29 Jun 2020 23:44:58: #2 predicted fragment length is 40 bps INFO @ Mon, 29 Jun 2020 23:44:58: #2 alternative fragment length(s) may be 40 bps INFO @ Mon, 29 Jun 2020 23:44:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287685/SRX287685.10_model.r WARNING @ Mon, 29 Jun 2020 23:44:58: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:44:58: #2 You may need to consider one of the other alternative d(s): 40 WARNING @ Mon, 29 Jun 2020 23:44:58: #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 23:44:58: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:44:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:45:03: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:45:06: 17000000 INFO @ Mon, 29 Jun 2020 23:45:14: 18000000 INFO @ Mon, 29 Jun 2020 23:45:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287685/SRX287685.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:45:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287685/SRX287685.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:45:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287685/SRX287685.05_summits.bed INFO @ Mon, 29 Jun 2020 23:45:22: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2268 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:45:23: 19000000 INFO @ Mon, 29 Jun 2020 23:45:32: 20000000 INFO @ Mon, 29 Jun 2020 23:45:33: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:45:41: 21000000 BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:45:49: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:45:49: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:45:49: #1 total tags in treatment: 21807111 INFO @ Mon, 29 Jun 2020 23:45:49: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:45:49: #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 23:45:49: #1 tags after filtering in treatment: 21807111 INFO @ Mon, 29 Jun 2020 23:45:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:45:49: #1 finished! INFO @ Mon, 29 Jun 2020 23:45:49: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:45:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:45:51: #2 number of paired peaks: 171 WARNING @ Mon, 29 Jun 2020 23:45:51: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Mon, 29 Jun 2020 23:45:51: start model_add_line... INFO @ Mon, 29 Jun 2020 23:45:51: start X-correlation... INFO @ Mon, 29 Jun 2020 23:45:51: end of X-cor INFO @ Mon, 29 Jun 2020 23:45:51: #2 finished! INFO @ Mon, 29 Jun 2020 23:45:51: #2 predicted fragment length is 40 bps INFO @ Mon, 29 Jun 2020 23:45:51: #2 alternative fragment length(s) may be 40 bps INFO @ Mon, 29 Jun 2020 23:45:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287685/SRX287685.20_model.r WARNING @ Mon, 29 Jun 2020 23:45:51: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:45:51: #2 You may need to consider one of the other alternative d(s): 40 WARNING @ Mon, 29 Jun 2020 23:45:51: #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 23:45:51: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:45:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:45:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287685/SRX287685.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:45:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287685/SRX287685.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:45:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287685/SRX287685.10_summits.bed INFO @ Mon, 29 Jun 2020 23:45:51: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1902 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:46:26: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:46:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287685/SRX287685.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:46:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287685/SRX287685.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:46:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287685/SRX287685.20_summits.bed INFO @ Mon, 29 Jun 2020 23:46:45: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1452 records, 4 fields): 8 millis CompletedMACS2peakCalling