Job ID = 6527777 SRX = SRX287572 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:29:56 prefetch.2.10.7: 1) Downloading 'SRR869715'... 2020-06-29T13:29:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:33:15 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:33:15 prefetch.2.10.7: 1) 'SRR869715' was downloaded successfully Read 26924228 spots for SRR869715/SRR869715.sra Written 26924228 spots for SRR869715/SRR869715.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 26924228 reads; of these: 26924228 (100.00%) were unpaired; of these: 1125884 (4.18%) aligned 0 times 17096963 (63.50%) aligned exactly 1 time 8701381 (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] 3992167 / 25798344 = 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 23:02:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287572/SRX287572.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287572/SRX287572.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287572/SRX287572.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287572/SRX287572.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 23:02:34: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:02:34: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:02:42: 1000000 INFO @ Mon, 29 Jun 2020 23:02:50: 2000000 INFO @ Mon, 29 Jun 2020 23:02:58: 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 @ Mon, 29 Jun 2020 23:03:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287572/SRX287572.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287572/SRX287572.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287572/SRX287572.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287572/SRX287572.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 23:03:04: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:03:04: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:03:06: 4000000 INFO @ Mon, 29 Jun 2020 23:03:12: 1000000 INFO @ Mon, 29 Jun 2020 23:03:14: 5000000 INFO @ Mon, 29 Jun 2020 23:03:20: 2000000 INFO @ Mon, 29 Jun 2020 23:03:23: 6000000 INFO @ Mon, 29 Jun 2020 23:03:28: 3000000 INFO @ Mon, 29 Jun 2020 23:03:31: 7000000 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 23:03:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287572/SRX287572.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287572/SRX287572.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287572/SRX287572.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287572/SRX287572.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 23:03:34: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:03:34: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:03:35: 4000000 INFO @ Mon, 29 Jun 2020 23:03:39: 8000000 INFO @ Mon, 29 Jun 2020 23:03:43: 1000000 INFO @ Mon, 29 Jun 2020 23:03:43: 5000000 INFO @ Mon, 29 Jun 2020 23:03:48: 9000000 INFO @ Mon, 29 Jun 2020 23:03:51: 6000000 INFO @ Mon, 29 Jun 2020 23:03:51: 2000000 INFO @ Mon, 29 Jun 2020 23:03:56: 10000000 INFO @ Mon, 29 Jun 2020 23:03:59: 7000000 INFO @ Mon, 29 Jun 2020 23:04:00: 3000000 INFO @ Mon, 29 Jun 2020 23:04:05: 11000000 INFO @ Mon, 29 Jun 2020 23:04:07: 8000000 INFO @ Mon, 29 Jun 2020 23:04:08: 4000000 INFO @ Mon, 29 Jun 2020 23:04:13: 12000000 INFO @ Mon, 29 Jun 2020 23:04:15: 9000000 INFO @ Mon, 29 Jun 2020 23:04:17: 5000000 INFO @ Mon, 29 Jun 2020 23:04:22: 13000000 INFO @ Mon, 29 Jun 2020 23:04:23: 10000000 INFO @ Mon, 29 Jun 2020 23:04:25: 6000000 INFO @ Mon, 29 Jun 2020 23:04:30: 14000000 INFO @ Mon, 29 Jun 2020 23:04:31: 11000000 INFO @ Mon, 29 Jun 2020 23:04:33: 7000000 INFO @ Mon, 29 Jun 2020 23:04:38: 15000000 INFO @ Mon, 29 Jun 2020 23:04:38: 12000000 INFO @ Mon, 29 Jun 2020 23:04:41: 8000000 INFO @ Mon, 29 Jun 2020 23:04:46: 13000000 INFO @ Mon, 29 Jun 2020 23:04:47: 16000000 INFO @ Mon, 29 Jun 2020 23:04:49: 9000000 INFO @ Mon, 29 Jun 2020 23:04:54: 14000000 INFO @ Mon, 29 Jun 2020 23:04:55: 17000000 INFO @ Mon, 29 Jun 2020 23:04:58: 10000000 INFO @ Mon, 29 Jun 2020 23:05:02: 15000000 INFO @ Mon, 29 Jun 2020 23:05:04: 18000000 INFO @ Mon, 29 Jun 2020 23:05:06: 11000000 INFO @ Mon, 29 Jun 2020 23:05:10: 16000000 INFO @ Mon, 29 Jun 2020 23:05:12: 19000000 INFO @ Mon, 29 Jun 2020 23:05:14: 12000000 INFO @ Mon, 29 Jun 2020 23:05:18: 17000000 INFO @ Mon, 29 Jun 2020 23:05:20: 20000000 INFO @ Mon, 29 Jun 2020 23:05:22: 13000000 INFO @ Mon, 29 Jun 2020 23:05:25: 18000000 INFO @ Mon, 29 Jun 2020 23:05:28: 21000000 INFO @ Mon, 29 Jun 2020 23:05:30: 14000000 INFO @ Mon, 29 Jun 2020 23:05:33: 19000000 INFO @ Mon, 29 Jun 2020 23:05:35: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:05:35: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:05:35: #1 total tags in treatment: 21806177 INFO @ Mon, 29 Jun 2020 23:05:35: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:05:35: #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 23:05:35: #1 tags after filtering in treatment: 21806177 INFO @ Mon, 29 Jun 2020 23:05:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:05:35: #1 finished! INFO @ Mon, 29 Jun 2020 23:05:35: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:05:35: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:05:36: #2 number of paired peaks: 162 WARNING @ Mon, 29 Jun 2020 23:05:36: Fewer paired peaks (162) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 162 pairs to build model! INFO @ Mon, 29 Jun 2020 23:05:36: start model_add_line... INFO @ Mon, 29 Jun 2020 23:05:37: start X-correlation... INFO @ Mon, 29 Jun 2020 23:05:37: end of X-cor INFO @ Mon, 29 Jun 2020 23:05:37: #2 finished! INFO @ Mon, 29 Jun 2020 23:05:37: #2 predicted fragment length is 40 bps INFO @ Mon, 29 Jun 2020 23:05:37: #2 alternative fragment length(s) may be 40 bps INFO @ Mon, 29 Jun 2020 23:05:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287572/SRX287572.05_model.r WARNING @ Mon, 29 Jun 2020 23:05:37: #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 23:05:37: #2 You may need to consider one of the other alternative d(s): 40 WARNING @ Mon, 29 Jun 2020 23:05:37: #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 23:05:37: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:05:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:05:38: 15000000 INFO @ Mon, 29 Jun 2020 23:05:41: 20000000 INFO @ Mon, 29 Jun 2020 23:05:45: 16000000 INFO @ Mon, 29 Jun 2020 23:05:49: 21000000 INFO @ Mon, 29 Jun 2020 23:05:53: 17000000 INFO @ Mon, 29 Jun 2020 23:05:55: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:05:55: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:05:55: #1 total tags in treatment: 21806177 INFO @ Mon, 29 Jun 2020 23:05:55: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:05:55: #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 23:05:56: #1 tags after filtering in treatment: 21806177 INFO @ Mon, 29 Jun 2020 23:05:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:05:56: #1 finished! INFO @ Mon, 29 Jun 2020 23:05:56: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:05:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:05:57: #2 number of paired peaks: 162 WARNING @ Mon, 29 Jun 2020 23:05:57: Fewer paired peaks (162) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 162 pairs to build model! INFO @ Mon, 29 Jun 2020 23:05:57: start model_add_line... INFO @ Mon, 29 Jun 2020 23:05:57: start X-correlation... INFO @ Mon, 29 Jun 2020 23:05:57: end of X-cor INFO @ Mon, 29 Jun 2020 23:05:57: #2 finished! INFO @ Mon, 29 Jun 2020 23:05:57: #2 predicted fragment length is 40 bps INFO @ Mon, 29 Jun 2020 23:05:57: #2 alternative fragment length(s) may be 40 bps INFO @ Mon, 29 Jun 2020 23:05:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287572/SRX287572.10_model.r WARNING @ Mon, 29 Jun 2020 23:05:57: #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 23:05:57: #2 You may need to consider one of the other alternative d(s): 40 WARNING @ Mon, 29 Jun 2020 23:05:57: #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 23:05:57: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:05:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:06:00: 18000000 INFO @ Mon, 29 Jun 2020 23:06:07: 19000000 INFO @ Mon, 29 Jun 2020 23:06:12: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:06:15: 20000000 INFO @ Mon, 29 Jun 2020 23:06:22: 21000000 INFO @ Mon, 29 Jun 2020 23:06:28: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:06:28: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:06:28: #1 total tags in treatment: 21806177 INFO @ Mon, 29 Jun 2020 23:06:28: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:06:28: #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 23:06:29: #1 tags after filtering in treatment: 21806177 INFO @ Mon, 29 Jun 2020 23:06:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:06:29: #1 finished! INFO @ Mon, 29 Jun 2020 23:06:29: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:06:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:06:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287572/SRX287572.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:06:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287572/SRX287572.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:06:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287572/SRX287572.05_summits.bed INFO @ Mon, 29 Jun 2020 23:06:30: Done! INFO @ Mon, 29 Jun 2020 23:06:30: #2 number of paired peaks: 162 WARNING @ Mon, 29 Jun 2020 23:06:30: Fewer paired peaks (162) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 162 pairs to build model! INFO @ Mon, 29 Jun 2020 23:06:30: start model_add_line... INFO @ Mon, 29 Jun 2020 23:06:30: start X-correlation... INFO @ Mon, 29 Jun 2020 23:06:30: end of X-cor INFO @ Mon, 29 Jun 2020 23:06:30: #2 finished! INFO @ Mon, 29 Jun 2020 23:06:30: #2 predicted fragment length is 40 bps INFO @ Mon, 29 Jun 2020 23:06:30: #2 alternative fragment length(s) may be 40 bps INFO @ Mon, 29 Jun 2020 23:06:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287572/SRX287572.20_model.r WARNING @ Mon, 29 Jun 2020 23:06:30: #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 23:06:30: #2 You may need to consider one of the other alternative d(s): 40 WARNING @ Mon, 29 Jun 2020 23:06:30: #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 23:06:30: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:06:30: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2273 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:06:32: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:06:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287572/SRX287572.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:06:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287572/SRX287572.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:06:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287572/SRX287572.10_summits.bed INFO @ Mon, 29 Jun 2020 23:06:50: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1901 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:07:05: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:07:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287572/SRX287572.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:07:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287572/SRX287572.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:07:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287572/SRX287572.20_summits.bed INFO @ Mon, 29 Jun 2020 23:07:23: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1434 records, 4 fields): 4 millis CompletedMACS2peakCalling