Job ID = 6368116 SRX = SRX466579 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:06:01 prefetch.2.10.7: 1) Downloading 'SRR1163645'... 2020-06-16T00:06:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:10:02 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:10:02 prefetch.2.10.7: 1) 'SRR1163645' was downloaded successfully Read 35457974 spots for SRR1163645/SRR1163645.sra Written 35457974 spots for SRR1163645/SRR1163645.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: 00:05:51 35457974 reads; of these: 35457974 (100.00%) were unpaired; of these: 4201436 (11.85%) aligned 0 times 23724063 (66.91%) aligned exactly 1 time 7532475 (21.24%) aligned >1 times 88.15% overall alignment rate Time searching: 00:05:51 Overall time: 00:05:51 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 7647186 / 31256538 = 0.2447 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 @ Tue, 16 Jun 2020 09:23:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466579/SRX466579.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466579/SRX466579.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466579/SRX466579.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466579/SRX466579.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 09:23:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:23:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:23:44: 1000000 INFO @ Tue, 16 Jun 2020 09:23:49: 2000000 INFO @ Tue, 16 Jun 2020 09:23:55: 3000000 INFO @ Tue, 16 Jun 2020 09:24:00: 4000000 INFO @ Tue, 16 Jun 2020 09:24:05: 5000000 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 @ Tue, 16 Jun 2020 09:24:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466579/SRX466579.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466579/SRX466579.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466579/SRX466579.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466579/SRX466579.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 09:24:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:24:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:24:10: 6000000 INFO @ Tue, 16 Jun 2020 09:24:15: 1000000 INFO @ Tue, 16 Jun 2020 09:24:15: 7000000 INFO @ Tue, 16 Jun 2020 09:24:20: 2000000 INFO @ Tue, 16 Jun 2020 09:24:21: 8000000 INFO @ Tue, 16 Jun 2020 09:24:26: 3000000 INFO @ Tue, 16 Jun 2020 09:24:26: 9000000 INFO @ Tue, 16 Jun 2020 09:24:31: 4000000 INFO @ Tue, 16 Jun 2020 09:24:31: 10000000 INFO @ Tue, 16 Jun 2020 09:24:36: 5000000 INFO @ Tue, 16 Jun 2020 09:24:37: 11000000 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 @ Tue, 16 Jun 2020 09:24:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466579/SRX466579.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466579/SRX466579.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466579/SRX466579.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466579/SRX466579.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 09:24:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:24:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:24:42: 6000000 INFO @ Tue, 16 Jun 2020 09:24:43: 12000000 INFO @ Tue, 16 Jun 2020 09:24:46: 1000000 INFO @ Tue, 16 Jun 2020 09:24:48: 7000000 INFO @ Tue, 16 Jun 2020 09:24:48: 13000000 INFO @ Tue, 16 Jun 2020 09:24:52: 2000000 INFO @ Tue, 16 Jun 2020 09:24:54: 8000000 INFO @ Tue, 16 Jun 2020 09:24:54: 14000000 INFO @ Tue, 16 Jun 2020 09:24:58: 3000000 INFO @ Tue, 16 Jun 2020 09:25:00: 9000000 INFO @ Tue, 16 Jun 2020 09:25:00: 15000000 INFO @ Tue, 16 Jun 2020 09:25:05: 4000000 INFO @ Tue, 16 Jun 2020 09:25:05: 10000000 INFO @ Tue, 16 Jun 2020 09:25:06: 16000000 INFO @ Tue, 16 Jun 2020 09:25:11: 5000000 INFO @ Tue, 16 Jun 2020 09:25:11: 11000000 INFO @ Tue, 16 Jun 2020 09:25:12: 17000000 INFO @ Tue, 16 Jun 2020 09:25:17: 12000000 INFO @ Tue, 16 Jun 2020 09:25:17: 6000000 INFO @ Tue, 16 Jun 2020 09:25:18: 18000000 INFO @ Tue, 16 Jun 2020 09:25:23: 13000000 INFO @ Tue, 16 Jun 2020 09:25:23: 7000000 INFO @ Tue, 16 Jun 2020 09:25:23: 19000000 INFO @ Tue, 16 Jun 2020 09:25:28: 14000000 INFO @ Tue, 16 Jun 2020 09:25:29: 8000000 INFO @ Tue, 16 Jun 2020 09:25:29: 20000000 INFO @ Tue, 16 Jun 2020 09:25:34: 15000000 INFO @ Tue, 16 Jun 2020 09:25:35: 21000000 INFO @ Tue, 16 Jun 2020 09:25:35: 9000000 INFO @ Tue, 16 Jun 2020 09:25:40: 16000000 INFO @ Tue, 16 Jun 2020 09:25:41: 22000000 INFO @ Tue, 16 Jun 2020 09:25:41: 10000000 INFO @ Tue, 16 Jun 2020 09:25:46: 17000000 INFO @ Tue, 16 Jun 2020 09:25:47: 23000000 INFO @ Tue, 16 Jun 2020 09:25:48: 11000000 INFO @ Tue, 16 Jun 2020 09:25:50: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:25:50: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:25:50: #1 total tags in treatment: 23609352 INFO @ Tue, 16 Jun 2020 09:25:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:25:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:25:51: #1 tags after filtering in treatment: 23609352 INFO @ Tue, 16 Jun 2020 09:25:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:25:51: #1 finished! INFO @ Tue, 16 Jun 2020 09:25:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:25:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:25:52: 18000000 INFO @ Tue, 16 Jun 2020 09:25:52: #2 number of paired peaks: 538 WARNING @ Tue, 16 Jun 2020 09:25:52: Fewer paired peaks (538) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 538 pairs to build model! INFO @ Tue, 16 Jun 2020 09:25:52: start model_add_line... INFO @ Tue, 16 Jun 2020 09:25:53: start X-correlation... INFO @ Tue, 16 Jun 2020 09:25:53: end of X-cor INFO @ Tue, 16 Jun 2020 09:25:53: #2 finished! INFO @ Tue, 16 Jun 2020 09:25:53: #2 predicted fragment length is 63 bps INFO @ Tue, 16 Jun 2020 09:25:53: #2 alternative fragment length(s) may be 2,40,63,74 bps INFO @ Tue, 16 Jun 2020 09:25:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466579/SRX466579.05_model.r WARNING @ Tue, 16 Jun 2020 09:25:53: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:25:53: #2 You may need to consider one of the other alternative d(s): 2,40,63,74 WARNING @ Tue, 16 Jun 2020 09:25:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:25:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:25:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:25:54: 12000000 INFO @ Tue, 16 Jun 2020 09:25:58: 19000000 INFO @ Tue, 16 Jun 2020 09:26:00: 13000000 INFO @ Tue, 16 Jun 2020 09:26:04: 20000000 INFO @ Tue, 16 Jun 2020 09:26:06: 14000000 INFO @ Tue, 16 Jun 2020 09:26:10: 21000000 INFO @ Tue, 16 Jun 2020 09:26:12: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:26:16: 22000000 INFO @ Tue, 16 Jun 2020 09:26:19: 16000000 INFO @ Tue, 16 Jun 2020 09:26:21: 23000000 INFO @ Tue, 16 Jun 2020 09:26:25: 17000000 INFO @ Tue, 16 Jun 2020 09:26:25: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:26:25: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:26:25: #1 total tags in treatment: 23609352 INFO @ Tue, 16 Jun 2020 09:26:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:26:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:26:26: #1 tags after filtering in treatment: 23609352 INFO @ Tue, 16 Jun 2020 09:26:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:26:26: #1 finished! INFO @ Tue, 16 Jun 2020 09:26:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:26:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:26:27: #2 number of paired peaks: 538 WARNING @ Tue, 16 Jun 2020 09:26:27: Fewer paired peaks (538) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 538 pairs to build model! INFO @ Tue, 16 Jun 2020 09:26:27: start model_add_line... INFO @ Tue, 16 Jun 2020 09:26:27: start X-correlation... INFO @ Tue, 16 Jun 2020 09:26:27: end of X-cor INFO @ Tue, 16 Jun 2020 09:26:27: #2 finished! INFO @ Tue, 16 Jun 2020 09:26:27: #2 predicted fragment length is 63 bps INFO @ Tue, 16 Jun 2020 09:26:27: #2 alternative fragment length(s) may be 2,40,63,74 bps INFO @ Tue, 16 Jun 2020 09:26:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466579/SRX466579.10_model.r WARNING @ Tue, 16 Jun 2020 09:26:27: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:26:27: #2 You may need to consider one of the other alternative d(s): 2,40,63,74 WARNING @ Tue, 16 Jun 2020 09:26:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:26:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:26:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:26:31: 18000000 INFO @ Tue, 16 Jun 2020 09:26:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:26:37: 19000000 INFO @ Tue, 16 Jun 2020 09:26:43: 20000000 INFO @ Tue, 16 Jun 2020 09:26:49: 21000000 INFO @ Tue, 16 Jun 2020 09:26:54: 22000000 INFO @ Tue, 16 Jun 2020 09:27:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466579/SRX466579.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:27:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466579/SRX466579.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:27:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466579/SRX466579.05_summits.bed INFO @ Tue, 16 Jun 2020 09:27:00: 23000000 INFO @ Tue, 16 Jun 2020 09:27:00: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (15152 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:27:04: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:27:04: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:27:04: #1 total tags in treatment: 23609352 INFO @ Tue, 16 Jun 2020 09:27:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:27:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:27:05: #1 tags after filtering in treatment: 23609352 INFO @ Tue, 16 Jun 2020 09:27:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:27:05: #1 finished! INFO @ Tue, 16 Jun 2020 09:27:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:27:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:27:06: #2 number of paired peaks: 538 WARNING @ Tue, 16 Jun 2020 09:27:06: Fewer paired peaks (538) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 538 pairs to build model! INFO @ Tue, 16 Jun 2020 09:27:06: start model_add_line... INFO @ Tue, 16 Jun 2020 09:27:06: start X-correlation... INFO @ Tue, 16 Jun 2020 09:27:06: end of X-cor INFO @ Tue, 16 Jun 2020 09:27:06: #2 finished! INFO @ Tue, 16 Jun 2020 09:27:06: #2 predicted fragment length is 63 bps INFO @ Tue, 16 Jun 2020 09:27:06: #2 alternative fragment length(s) may be 2,40,63,74 bps INFO @ Tue, 16 Jun 2020 09:27:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466579/SRX466579.20_model.r WARNING @ Tue, 16 Jun 2020 09:27:06: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:27:06: #2 You may need to consider one of the other alternative d(s): 2,40,63,74 WARNING @ Tue, 16 Jun 2020 09:27:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:27:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:27:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:27:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:27:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466579/SRX466579.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:27:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466579/SRX466579.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:27:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466579/SRX466579.10_summits.bed INFO @ Tue, 16 Jun 2020 09:27:36: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (7711 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:27:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:28:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466579/SRX466579.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:28:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466579/SRX466579.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:28:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466579/SRX466579.20_summits.bed INFO @ Tue, 16 Jun 2020 09:28:13: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (2598 records, 4 fields): 4 millis CompletedMACS2peakCalling