Job ID = 6527830 SRX = SRX287802 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:37:25 prefetch.2.10.7: 1) Downloading 'SRR869991'... 2020-06-29T13:37:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:40:44 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:40:44 prefetch.2.10.7: 1) 'SRR869991' was downloaded successfully Read 23008083 spots for SRR869991/SRR869991.sra Written 23008083 spots for SRR869991/SRR869991.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: 00:08:27 23008083 reads; of these: 23008083 (100.00%) were unpaired; of these: 1291496 (5.61%) aligned 0 times 14514811 (63.09%) aligned exactly 1 time 7201776 (31.30%) aligned >1 times 94.39% overall alignment rate Time searching: 00:08:27 Overall time: 00:08:27 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] 3392752 / 21716587 = 0.1562 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 23:00:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287802/SRX287802.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287802/SRX287802.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287802/SRX287802.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287802/SRX287802.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 23:00:54: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:00:54: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:00:59: 1000000 INFO @ Mon, 29 Jun 2020 23:01:03: 2000000 INFO @ Mon, 29 Jun 2020 23:01:08: 3000000 INFO @ Mon, 29 Jun 2020 23:01:13: 4000000 INFO @ Mon, 29 Jun 2020 23:01:18: 5000000 INFO @ Mon, 29 Jun 2020 23:01:22: 6000000 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 23:01:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287802/SRX287802.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287802/SRX287802.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287802/SRX287802.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287802/SRX287802.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 23:01:24: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:01:24: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:01:27: 7000000 INFO @ Mon, 29 Jun 2020 23:01:30: 1000000 INFO @ Mon, 29 Jun 2020 23:01:32: 8000000 INFO @ Mon, 29 Jun 2020 23:01:35: 2000000 INFO @ Mon, 29 Jun 2020 23:01:36: 9000000 INFO @ Mon, 29 Jun 2020 23:01:41: 3000000 INFO @ Mon, 29 Jun 2020 23:01:41: 10000000 INFO @ Mon, 29 Jun 2020 23:01:46: 11000000 INFO @ Mon, 29 Jun 2020 23:01:46: 4000000 INFO @ Mon, 29 Jun 2020 23:01:50: 12000000 INFO @ Mon, 29 Jun 2020 23:01:52: 5000000 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 23:01:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287802/SRX287802.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287802/SRX287802.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287802/SRX287802.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287802/SRX287802.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 23:01:54: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:01:54: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:01:55: 13000000 INFO @ Mon, 29 Jun 2020 23:01:57: 6000000 INFO @ Mon, 29 Jun 2020 23:02:00: 1000000 INFO @ Mon, 29 Jun 2020 23:02:00: 14000000 INFO @ Mon, 29 Jun 2020 23:02:03: 7000000 INFO @ Mon, 29 Jun 2020 23:02:05: 15000000 INFO @ Mon, 29 Jun 2020 23:02:05: 2000000 INFO @ Mon, 29 Jun 2020 23:02:08: 8000000 INFO @ Mon, 29 Jun 2020 23:02:10: 16000000 INFO @ Mon, 29 Jun 2020 23:02:11: 3000000 INFO @ Mon, 29 Jun 2020 23:02:14: 9000000 INFO @ Mon, 29 Jun 2020 23:02:14: 17000000 INFO @ Mon, 29 Jun 2020 23:02:16: 4000000 INFO @ Mon, 29 Jun 2020 23:02:19: 18000000 INFO @ Mon, 29 Jun 2020 23:02:19: 10000000 INFO @ Mon, 29 Jun 2020 23:02:21: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:02:21: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:02:21: #1 total tags in treatment: 18323835 INFO @ Mon, 29 Jun 2020 23:02:21: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:02:21: #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 23:02:21: #1 tags after filtering in treatment: 18323835 INFO @ Mon, 29 Jun 2020 23:02:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:02:21: #1 finished! INFO @ Mon, 29 Jun 2020 23:02:21: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:02:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:02:22: 5000000 INFO @ Mon, 29 Jun 2020 23:02:22: #2 number of paired peaks: 154 WARNING @ Mon, 29 Jun 2020 23:02:22: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Mon, 29 Jun 2020 23:02:22: start model_add_line... INFO @ Mon, 29 Jun 2020 23:02:22: start X-correlation... INFO @ Mon, 29 Jun 2020 23:02:22: end of X-cor INFO @ Mon, 29 Jun 2020 23:02:22: #2 finished! INFO @ Mon, 29 Jun 2020 23:02:22: #2 predicted fragment length is 47 bps INFO @ Mon, 29 Jun 2020 23:02:22: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 29 Jun 2020 23:02:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287802/SRX287802.05_model.r WARNING @ Mon, 29 Jun 2020 23:02:22: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:02:22: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 29 Jun 2020 23:02:22: #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 23:02:22: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:02:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:02:25: 11000000 INFO @ Mon, 29 Jun 2020 23:02:27: 6000000 INFO @ Mon, 29 Jun 2020 23:02:30: 12000000 INFO @ Mon, 29 Jun 2020 23:02:33: 7000000 INFO @ Mon, 29 Jun 2020 23:02:36: 13000000 INFO @ Mon, 29 Jun 2020 23:02:38: 8000000 INFO @ Mon, 29 Jun 2020 23:02:41: 14000000 INFO @ Mon, 29 Jun 2020 23:02:44: 9000000 INFO @ Mon, 29 Jun 2020 23:02:47: 15000000 INFO @ Mon, 29 Jun 2020 23:02:49: 10000000 INFO @ Mon, 29 Jun 2020 23:02:52: 16000000 INFO @ Mon, 29 Jun 2020 23:02:55: 11000000 INFO @ Mon, 29 Jun 2020 23:02:56: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:02:58: 17000000 INFO @ Mon, 29 Jun 2020 23:03:00: 12000000 INFO @ Mon, 29 Jun 2020 23:03:04: 18000000 INFO @ Mon, 29 Jun 2020 23:03:05: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:03:05: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:03:05: #1 total tags in treatment: 18323835 INFO @ Mon, 29 Jun 2020 23:03:05: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:03:05: #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 23:03:06: #1 tags after filtering in treatment: 18323835 INFO @ Mon, 29 Jun 2020 23:03:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:03:06: #1 finished! INFO @ Mon, 29 Jun 2020 23:03:06: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:03:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:03:06: 13000000 INFO @ Mon, 29 Jun 2020 23:03:07: #2 number of paired peaks: 154 WARNING @ Mon, 29 Jun 2020 23:03:07: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Mon, 29 Jun 2020 23:03:07: start model_add_line... INFO @ Mon, 29 Jun 2020 23:03:07: start X-correlation... INFO @ Mon, 29 Jun 2020 23:03:07: end of X-cor INFO @ Mon, 29 Jun 2020 23:03:07: #2 finished! INFO @ Mon, 29 Jun 2020 23:03:07: #2 predicted fragment length is 47 bps INFO @ Mon, 29 Jun 2020 23:03:07: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 29 Jun 2020 23:03:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287802/SRX287802.10_model.r WARNING @ Mon, 29 Jun 2020 23:03:07: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:03:07: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 29 Jun 2020 23:03:07: #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 23:03:07: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:03:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:03:11: 14000000 INFO @ Mon, 29 Jun 2020 23:03:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287802/SRX287802.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:03:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287802/SRX287802.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:03:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287802/SRX287802.05_summits.bed INFO @ Mon, 29 Jun 2020 23:03:13: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2169 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:03:17: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:03:22: 16000000 INFO @ Mon, 29 Jun 2020 23:03:28: 17000000 INFO @ Mon, 29 Jun 2020 23:03:33: 18000000 INFO @ Mon, 29 Jun 2020 23:03:34: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:03:34: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:03:34: #1 total tags in treatment: 18323835 INFO @ Mon, 29 Jun 2020 23:03:34: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:03:34: #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 23:03:35: #1 tags after filtering in treatment: 18323835 INFO @ Mon, 29 Jun 2020 23:03:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:03:35: #1 finished! INFO @ Mon, 29 Jun 2020 23:03:35: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:03:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:03:36: #2 number of paired peaks: 154 WARNING @ Mon, 29 Jun 2020 23:03:36: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Mon, 29 Jun 2020 23:03:36: start model_add_line... INFO @ Mon, 29 Jun 2020 23:03:36: start X-correlation... INFO @ Mon, 29 Jun 2020 23:03:36: end of X-cor INFO @ Mon, 29 Jun 2020 23:03:36: #2 finished! INFO @ Mon, 29 Jun 2020 23:03:36: #2 predicted fragment length is 47 bps INFO @ Mon, 29 Jun 2020 23:03:36: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 29 Jun 2020 23:03:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287802/SRX287802.20_model.r WARNING @ Mon, 29 Jun 2020 23:03:36: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:03:36: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 29 Jun 2020 23:03:36: #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 23:03:36: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:03:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:03:40: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:03:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287802/SRX287802.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:03:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287802/SRX287802.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:03:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287802/SRX287802.10_summits.bed INFO @ Mon, 29 Jun 2020 23:03:57: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1784 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:04:09: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:04:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287802/SRX287802.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:04:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287802/SRX287802.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:04:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287802/SRX287802.20_summits.bed INFO @ Mon, 29 Jun 2020 23:04:26: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1357 records, 4 fields): 2 millis CompletedMACS2peakCalling