Job ID = 6527606 SRX = SRX1361345 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:45:36 prefetch.2.10.7: 1) Downloading 'SRR2749783'... 2020-06-29T12:45:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:49:25 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:49:25 prefetch.2.10.7: 1) 'SRR2749783' was downloaded successfully Read 41756437 spots for SRR2749783/SRR2749783.sra Written 41756437 spots for SRR2749783/SRR2749783.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: 00:22:12 41756437 reads; of these: 41756437 (100.00%) were unpaired; of these: 1377928 (3.30%) aligned 0 times 15976810 (38.26%) aligned exactly 1 time 24401699 (58.44%) aligned >1 times 96.70% overall alignment rate Time searching: 00:22:12 Overall time: 00:22:12 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 20 files... [bam_rmdupse_core] 13459992 / 40378509 = 0.3333 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 22:37:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1361345/SRX1361345.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1361345/SRX1361345.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1361345/SRX1361345.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1361345/SRX1361345.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 22:37:56: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:37:56: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:38:03: 1000000 INFO @ Mon, 29 Jun 2020 22:38:09: 2000000 INFO @ Mon, 29 Jun 2020 22:38:15: 3000000 INFO @ Mon, 29 Jun 2020 22:38:21: 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 @ Mon, 29 Jun 2020 22:38:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1361345/SRX1361345.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1361345/SRX1361345.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1361345/SRX1361345.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1361345/SRX1361345.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 22:38:26: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:38:26: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:38:27: 5000000 INFO @ Mon, 29 Jun 2020 22:38:32: 6000000 INFO @ Mon, 29 Jun 2020 22:38:33: 1000000 INFO @ Mon, 29 Jun 2020 22:38:38: 7000000 INFO @ Mon, 29 Jun 2020 22:38:40: 2000000 INFO @ Mon, 29 Jun 2020 22:38:44: 8000000 INFO @ Mon, 29 Jun 2020 22:38:47: 3000000 INFO @ Mon, 29 Jun 2020 22:38:50: 9000000 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 22:38:54: 4000000 INFO @ Mon, 29 Jun 2020 22:38:56: 10000000 INFO @ Mon, 29 Jun 2020 22:38:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1361345/SRX1361345.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1361345/SRX1361345.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1361345/SRX1361345.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1361345/SRX1361345.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 22:38:56: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:38:56: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:39:01: 5000000 INFO @ Mon, 29 Jun 2020 22:39:01: 11000000 INFO @ Mon, 29 Jun 2020 22:39:03: 1000000 INFO @ Mon, 29 Jun 2020 22:39:07: 12000000 INFO @ Mon, 29 Jun 2020 22:39:08: 6000000 INFO @ Mon, 29 Jun 2020 22:39:10: 2000000 INFO @ Mon, 29 Jun 2020 22:39:13: 13000000 INFO @ Mon, 29 Jun 2020 22:39:15: 7000000 INFO @ Mon, 29 Jun 2020 22:39:17: 3000000 INFO @ Mon, 29 Jun 2020 22:39:19: 14000000 INFO @ Mon, 29 Jun 2020 22:39:22: 8000000 INFO @ Mon, 29 Jun 2020 22:39:24: 4000000 INFO @ Mon, 29 Jun 2020 22:39:24: 15000000 INFO @ Mon, 29 Jun 2020 22:39:28: 9000000 INFO @ Mon, 29 Jun 2020 22:39:30: 16000000 INFO @ Mon, 29 Jun 2020 22:39:31: 5000000 INFO @ Mon, 29 Jun 2020 22:39:35: 10000000 INFO @ Mon, 29 Jun 2020 22:39:36: 17000000 INFO @ Mon, 29 Jun 2020 22:39:38: 6000000 INFO @ Mon, 29 Jun 2020 22:39:41: 18000000 INFO @ Mon, 29 Jun 2020 22:39:42: 11000000 INFO @ Mon, 29 Jun 2020 22:39:44: 7000000 INFO @ Mon, 29 Jun 2020 22:39:46: 19000000 INFO @ Mon, 29 Jun 2020 22:39:48: 12000000 INFO @ Mon, 29 Jun 2020 22:39:50: 8000000 INFO @ Mon, 29 Jun 2020 22:39:52: 20000000 INFO @ Mon, 29 Jun 2020 22:39:54: 13000000 INFO @ Mon, 29 Jun 2020 22:39:56: 9000000 INFO @ Mon, 29 Jun 2020 22:39:57: 21000000 INFO @ Mon, 29 Jun 2020 22:39:59: 14000000 INFO @ Mon, 29 Jun 2020 22:40:02: 10000000 INFO @ Mon, 29 Jun 2020 22:40:03: 22000000 INFO @ Mon, 29 Jun 2020 22:40:05: 15000000 INFO @ Mon, 29 Jun 2020 22:40:08: 23000000 INFO @ Mon, 29 Jun 2020 22:40:08: 11000000 INFO @ Mon, 29 Jun 2020 22:40:11: 16000000 INFO @ Mon, 29 Jun 2020 22:40:13: 24000000 INFO @ Mon, 29 Jun 2020 22:40:14: 12000000 INFO @ Mon, 29 Jun 2020 22:40:17: 17000000 INFO @ Mon, 29 Jun 2020 22:40:18: 25000000 INFO @ Mon, 29 Jun 2020 22:40:19: 13000000 INFO @ Mon, 29 Jun 2020 22:40:23: 26000000 INFO @ Mon, 29 Jun 2020 22:40:23: 18000000 INFO @ Mon, 29 Jun 2020 22:40:25: 14000000 INFO @ Mon, 29 Jun 2020 22:40:28: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:40:28: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:40:28: #1 total tags in treatment: 26918517 INFO @ Mon, 29 Jun 2020 22:40:28: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:40:28: #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 22:40:28: #1 tags after filtering in treatment: 26918517 INFO @ Mon, 29 Jun 2020 22:40:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:40:28: #1 finished! INFO @ Mon, 29 Jun 2020 22:40:28: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:40:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:40:29: 19000000 INFO @ Mon, 29 Jun 2020 22:40:30: #2 number of paired peaks: 439 WARNING @ Mon, 29 Jun 2020 22:40:30: Fewer paired peaks (439) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 439 pairs to build model! INFO @ Mon, 29 Jun 2020 22:40:30: start model_add_line... INFO @ Mon, 29 Jun 2020 22:40:30: start X-correlation... INFO @ Mon, 29 Jun 2020 22:40:30: end of X-cor INFO @ Mon, 29 Jun 2020 22:40:30: #2 finished! INFO @ Mon, 29 Jun 2020 22:40:30: #2 predicted fragment length is 30 bps INFO @ Mon, 29 Jun 2020 22:40:30: #2 alternative fragment length(s) may be 2,30,511 bps INFO @ Mon, 29 Jun 2020 22:40:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1361345/SRX1361345.05_model.r WARNING @ Mon, 29 Jun 2020 22:40:31: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:40:31: #2 You may need to consider one of the other alternative d(s): 2,30,511 WARNING @ Mon, 29 Jun 2020 22:40:31: #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 22:40:31: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:40:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:40:31: 15000000 INFO @ Mon, 29 Jun 2020 22:40:35: 20000000 INFO @ Mon, 29 Jun 2020 22:40:37: 16000000 INFO @ Mon, 29 Jun 2020 22:40:41: 21000000 INFO @ Mon, 29 Jun 2020 22:40:43: 17000000 INFO @ Mon, 29 Jun 2020 22:40:47: 22000000 INFO @ Mon, 29 Jun 2020 22:40:49: 18000000 INFO @ Mon, 29 Jun 2020 22:40:52: 23000000 INFO @ Mon, 29 Jun 2020 22:40:55: 19000000 INFO @ Mon, 29 Jun 2020 22:40:58: 24000000 INFO @ Mon, 29 Jun 2020 22:41:01: 20000000 INFO @ Mon, 29 Jun 2020 22:41:04: 25000000 INFO @ Mon, 29 Jun 2020 22:41:07: 21000000 INFO @ Mon, 29 Jun 2020 22:41:10: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:41:12: 22000000 INFO @ Mon, 29 Jun 2020 22:41:15: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:41:15: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:41:15: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:41:15: #1 total tags in treatment: 26918517 INFO @ Mon, 29 Jun 2020 22:41:15: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:41:15: #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 22:41:16: #1 tags after filtering in treatment: 26918517 INFO @ Mon, 29 Jun 2020 22:41:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:41:16: #1 finished! INFO @ Mon, 29 Jun 2020 22:41:16: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:41:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:41:18: #2 number of paired peaks: 439 WARNING @ Mon, 29 Jun 2020 22:41:18: Fewer paired peaks (439) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 439 pairs to build model! INFO @ Mon, 29 Jun 2020 22:41:18: start model_add_line... INFO @ Mon, 29 Jun 2020 22:41:18: 23000000 INFO @ Mon, 29 Jun 2020 22:41:18: start X-correlation... INFO @ Mon, 29 Jun 2020 22:41:18: end of X-cor INFO @ Mon, 29 Jun 2020 22:41:18: #2 finished! INFO @ Mon, 29 Jun 2020 22:41:18: #2 predicted fragment length is 30 bps INFO @ Mon, 29 Jun 2020 22:41:18: #2 alternative fragment length(s) may be 2,30,511 bps INFO @ Mon, 29 Jun 2020 22:41:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1361345/SRX1361345.10_model.r WARNING @ Mon, 29 Jun 2020 22:41:18: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:41:18: #2 You may need to consider one of the other alternative d(s): 2,30,511 WARNING @ Mon, 29 Jun 2020 22:41:18: #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 22:41:18: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:41:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:41:23: 24000000 INFO @ Mon, 29 Jun 2020 22:41:28: 25000000 INFO @ Mon, 29 Jun 2020 22:41:33: 26000000 INFO @ Mon, 29 Jun 2020 22:41:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1361345/SRX1361345.05_peaks.xls INFO @ Mon, 29 Jun 2020 22:41:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1361345/SRX1361345.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:41:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1361345/SRX1361345.05_summits.bed INFO @ Mon, 29 Jun 2020 22:41:38: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (11484 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:41:38: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:41:38: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:41:38: #1 total tags in treatment: 26918517 INFO @ Mon, 29 Jun 2020 22:41:38: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:41:38: #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 22:41:39: #1 tags after filtering in treatment: 26918517 INFO @ Mon, 29 Jun 2020 22:41:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:41:39: #1 finished! INFO @ Mon, 29 Jun 2020 22:41:39: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:41:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:41:41: #2 number of paired peaks: 439 WARNING @ Mon, 29 Jun 2020 22:41:41: Fewer paired peaks (439) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 439 pairs to build model! INFO @ Mon, 29 Jun 2020 22:41:41: start model_add_line... INFO @ Mon, 29 Jun 2020 22:41:41: start X-correlation... INFO @ Mon, 29 Jun 2020 22:41:41: end of X-cor INFO @ Mon, 29 Jun 2020 22:41:41: #2 finished! INFO @ Mon, 29 Jun 2020 22:41:41: #2 predicted fragment length is 30 bps INFO @ Mon, 29 Jun 2020 22:41:41: #2 alternative fragment length(s) may be 2,30,511 bps INFO @ Mon, 29 Jun 2020 22:41:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1361345/SRX1361345.20_model.r WARNING @ Mon, 29 Jun 2020 22:41:41: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:41:41: #2 You may need to consider one of the other alternative d(s): 2,30,511 WARNING @ Mon, 29 Jun 2020 22:41:41: #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 22:41:41: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:41:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:42:03: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 22:42:26: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:42:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1361345/SRX1361345.10_peaks.xls INFO @ Mon, 29 Jun 2020 22:42:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1361345/SRX1361345.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:42:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1361345/SRX1361345.10_summits.bed INFO @ Mon, 29 Jun 2020 22:42:27: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3023 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:42:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1361345/SRX1361345.20_peaks.xls INFO @ Mon, 29 Jun 2020 22:42:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1361345/SRX1361345.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:42:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1361345/SRX1361345.20_summits.bed INFO @ Mon, 29 Jun 2020 22:42:50: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (917 records, 4 fields): 4 millis CompletedMACS2peakCalling