Job ID = 6366294 SRX = SRX1078718 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:45:52 prefetch.2.10.7: 1) Downloading 'SRR2084325'... 2020-06-15T22:45:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:48:57 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:48:57 prefetch.2.10.7: 1) 'SRR2084325' was downloaded successfully Read 24998257 spots for SRR2084325/SRR2084325.sra Written 24998257 spots for SRR2084325/SRR2084325.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: 00:05:38 24998257 reads; of these: 24998257 (100.00%) were unpaired; of these: 302223 (1.21%) aligned 0 times 20672722 (82.70%) aligned exactly 1 time 4023312 (16.09%) aligned >1 times 98.79% overall alignment rate Time searching: 00:05:38 Overall time: 00:05:38 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 12 files... [bam_rmdupse_core] 5613173 / 24696034 = 0.2273 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 08:02:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078718/SRX1078718.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078718/SRX1078718.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078718/SRX1078718.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078718/SRX1078718.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 08:02:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:02:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:02:13: 1000000 INFO @ Tue, 16 Jun 2020 08:02:19: 2000000 INFO @ Tue, 16 Jun 2020 08:02:24: 3000000 INFO @ Tue, 16 Jun 2020 08:02:30: 4000000 INFO @ Tue, 16 Jun 2020 08:02:35: 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 08:02:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078718/SRX1078718.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078718/SRX1078718.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078718/SRX1078718.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078718/SRX1078718.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 08:02:38: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:02:38: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:02:40: 6000000 INFO @ Tue, 16 Jun 2020 08:02:44: 1000000 INFO @ Tue, 16 Jun 2020 08:02:46: 7000000 INFO @ Tue, 16 Jun 2020 08:02:50: 2000000 INFO @ Tue, 16 Jun 2020 08:02:51: 8000000 INFO @ Tue, 16 Jun 2020 08:02:55: 3000000 INFO @ Tue, 16 Jun 2020 08:02:57: 9000000 INFO @ Tue, 16 Jun 2020 08:03:01: 4000000 INFO @ Tue, 16 Jun 2020 08:03:02: 10000000 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 08:03:07: 5000000 INFO @ Tue, 16 Jun 2020 08:03:08: 11000000 INFO @ Tue, 16 Jun 2020 08:03:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078718/SRX1078718.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078718/SRX1078718.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078718/SRX1078718.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078718/SRX1078718.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 08:03:08: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:03:08: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:03:13: 6000000 INFO @ Tue, 16 Jun 2020 08:03:13: 12000000 INFO @ Tue, 16 Jun 2020 08:03:14: 1000000 INFO @ Tue, 16 Jun 2020 08:03:18: 7000000 INFO @ Tue, 16 Jun 2020 08:03:18: 13000000 INFO @ Tue, 16 Jun 2020 08:03:20: 2000000 INFO @ Tue, 16 Jun 2020 08:03:24: 14000000 INFO @ Tue, 16 Jun 2020 08:03:24: 8000000 INFO @ Tue, 16 Jun 2020 08:03:25: 3000000 INFO @ Tue, 16 Jun 2020 08:03:29: 15000000 INFO @ Tue, 16 Jun 2020 08:03:30: 9000000 INFO @ Tue, 16 Jun 2020 08:03:31: 4000000 INFO @ Tue, 16 Jun 2020 08:03:34: 16000000 INFO @ Tue, 16 Jun 2020 08:03:36: 10000000 INFO @ Tue, 16 Jun 2020 08:03:37: 5000000 INFO @ Tue, 16 Jun 2020 08:03:39: 17000000 INFO @ Tue, 16 Jun 2020 08:03:41: 11000000 INFO @ Tue, 16 Jun 2020 08:03:43: 6000000 INFO @ Tue, 16 Jun 2020 08:03:44: 18000000 INFO @ Tue, 16 Jun 2020 08:03:47: 12000000 INFO @ Tue, 16 Jun 2020 08:03:48: 7000000 INFO @ Tue, 16 Jun 2020 08:03:50: 19000000 INFO @ Tue, 16 Jun 2020 08:03:50: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:03:50: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:03:50: #1 total tags in treatment: 19082861 INFO @ Tue, 16 Jun 2020 08:03:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:03:50: #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 08:03:51: #1 tags after filtering in treatment: 19082861 INFO @ Tue, 16 Jun 2020 08:03:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:03:51: #1 finished! INFO @ Tue, 16 Jun 2020 08:03:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:03:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:03:52: #2 number of paired peaks: 255 WARNING @ Tue, 16 Jun 2020 08:03:52: Fewer paired peaks (255) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 255 pairs to build model! INFO @ Tue, 16 Jun 2020 08:03:52: start model_add_line... INFO @ Tue, 16 Jun 2020 08:03:52: start X-correlation... INFO @ Tue, 16 Jun 2020 08:03:52: end of X-cor INFO @ Tue, 16 Jun 2020 08:03:52: #2 finished! INFO @ Tue, 16 Jun 2020 08:03:52: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:03:52: #2 alternative fragment length(s) may be 1,49 bps INFO @ Tue, 16 Jun 2020 08:03:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078718/SRX1078718.05_model.r WARNING @ Tue, 16 Jun 2020 08:03:52: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:03:52: #2 You may need to consider one of the other alternative d(s): 1,49 WARNING @ Tue, 16 Jun 2020 08:03:52: #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 08:03:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:03:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:03:53: 13000000 INFO @ Tue, 16 Jun 2020 08:03:54: 8000000 INFO @ Tue, 16 Jun 2020 08:03:59: 14000000 INFO @ Tue, 16 Jun 2020 08:04:00: 9000000 INFO @ Tue, 16 Jun 2020 08:04:04: 15000000 INFO @ Tue, 16 Jun 2020 08:04:06: 10000000 INFO @ Tue, 16 Jun 2020 08:04:10: 16000000 INFO @ Tue, 16 Jun 2020 08:04:11: 11000000 INFO @ Tue, 16 Jun 2020 08:04:15: 17000000 INFO @ Tue, 16 Jun 2020 08:04:17: 12000000 INFO @ Tue, 16 Jun 2020 08:04:21: 18000000 INFO @ Tue, 16 Jun 2020 08:04:23: 13000000 INFO @ Tue, 16 Jun 2020 08:04:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:04:27: 19000000 INFO @ Tue, 16 Jun 2020 08:04:27: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:04:27: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:04:27: #1 total tags in treatment: 19082861 INFO @ Tue, 16 Jun 2020 08:04:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:04:27: #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 08:04:28: #1 tags after filtering in treatment: 19082861 INFO @ Tue, 16 Jun 2020 08:04:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:04:28: #1 finished! INFO @ Tue, 16 Jun 2020 08:04:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:04:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:04:29: 14000000 INFO @ Tue, 16 Jun 2020 08:04:29: #2 number of paired peaks: 255 WARNING @ Tue, 16 Jun 2020 08:04:29: Fewer paired peaks (255) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 255 pairs to build model! INFO @ Tue, 16 Jun 2020 08:04:29: start model_add_line... INFO @ Tue, 16 Jun 2020 08:04:29: start X-correlation... INFO @ Tue, 16 Jun 2020 08:04:29: end of X-cor INFO @ Tue, 16 Jun 2020 08:04:29: #2 finished! INFO @ Tue, 16 Jun 2020 08:04:29: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:04:29: #2 alternative fragment length(s) may be 1,49 bps INFO @ Tue, 16 Jun 2020 08:04:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078718/SRX1078718.10_model.r WARNING @ Tue, 16 Jun 2020 08:04:29: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:04:29: #2 You may need to consider one of the other alternative d(s): 1,49 WARNING @ Tue, 16 Jun 2020 08:04:29: #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 08:04:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:04:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:04:34: 15000000 INFO @ Tue, 16 Jun 2020 08:04:40: 16000000 INFO @ Tue, 16 Jun 2020 08:04:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1078718/SRX1078718.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:04:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1078718/SRX1078718.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:04:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1078718/SRX1078718.05_summits.bed INFO @ Tue, 16 Jun 2020 08:04:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (739 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:04:45: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:04:51: 18000000 INFO @ Tue, 16 Jun 2020 08:04:57: 19000000 INFO @ Tue, 16 Jun 2020 08:04:57: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:04:57: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:04:57: #1 total tags in treatment: 19082861 INFO @ Tue, 16 Jun 2020 08:04:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:04:57: #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 08:04:58: #1 tags after filtering in treatment: 19082861 INFO @ Tue, 16 Jun 2020 08:04:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:04:58: #1 finished! INFO @ Tue, 16 Jun 2020 08:04:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:04:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:04:59: #2 number of paired peaks: 255 WARNING @ Tue, 16 Jun 2020 08:04:59: Fewer paired peaks (255) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 255 pairs to build model! INFO @ Tue, 16 Jun 2020 08:04:59: start model_add_line... INFO @ Tue, 16 Jun 2020 08:04:59: start X-correlation... INFO @ Tue, 16 Jun 2020 08:04:59: end of X-cor INFO @ Tue, 16 Jun 2020 08:04:59: #2 finished! INFO @ Tue, 16 Jun 2020 08:04:59: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:04:59: #2 alternative fragment length(s) may be 1,49 bps INFO @ Tue, 16 Jun 2020 08:04:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078718/SRX1078718.20_model.r WARNING @ Tue, 16 Jun 2020 08:04:59: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:04:59: #2 You may need to consider one of the other alternative d(s): 1,49 WARNING @ Tue, 16 Jun 2020 08:04:59: #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 08:04:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:04:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:05:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:05:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1078718/SRX1078718.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:05:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1078718/SRX1078718.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:05:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1078718/SRX1078718.10_summits.bed INFO @ Tue, 16 Jun 2020 08:05:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (482 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:05:31: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:05:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1078718/SRX1078718.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:05:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1078718/SRX1078718.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:05:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1078718/SRX1078718.20_summits.bed INFO @ Tue, 16 Jun 2020 08:05:46: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (178 records, 4 fields): 1 millis CompletedMACS2peakCalling