Job ID = 6367842 SRX = SRX4085410 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:32:50 prefetch.2.10.7: 1) Downloading 'SRR7167439'... 2020-06-15T23:32:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:41:22 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:41:22 prefetch.2.10.7: 1) 'SRR7167439' was downloaded successfully Read 20844202 spots for SRR7167439/SRR7167439.sra Written 20844202 spots for SRR7167439/SRR7167439.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: 00:11:03 20844202 reads; of these: 20844202 (100.00%) were paired; of these: 14110893 (67.70%) aligned concordantly 0 times 5783193 (27.74%) aligned concordantly exactly 1 time 950116 (4.56%) aligned concordantly >1 times ---- 14110893 pairs aligned concordantly 0 times; of these: 313372 (2.22%) aligned discordantly 1 time ---- 13797521 pairs aligned 0 times concordantly or discordantly; of these: 27595042 mates make up the pairs; of these: 22142884 (80.24%) aligned 0 times 4875608 (17.67%) aligned exactly 1 time 576550 (2.09%) aligned >1 times 46.88% overall alignment rate Time searching: 00:11:03 Overall time: 00:11:03 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 1847618 / 6940537 = 0.2662 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 09:01:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085410/SRX4085410.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085410/SRX4085410.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085410/SRX4085410.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085410/SRX4085410.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 09:01:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:01:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:01:37: 1000000 INFO @ Tue, 16 Jun 2020 09:01:41: 2000000 INFO @ Tue, 16 Jun 2020 09:01:46: 3000000 INFO @ Tue, 16 Jun 2020 09:01:51: 4000000 INFO @ Tue, 16 Jun 2020 09:01:55: 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 09:02:00: 6000000 INFO @ Tue, 16 Jun 2020 09:02:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085410/SRX4085410.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085410/SRX4085410.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085410/SRX4085410.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085410/SRX4085410.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 09:02:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:02:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:02:05: 7000000 INFO @ Tue, 16 Jun 2020 09:02:07: 1000000 INFO @ Tue, 16 Jun 2020 09:02:10: 8000000 INFO @ Tue, 16 Jun 2020 09:02:11: 2000000 INFO @ Tue, 16 Jun 2020 09:02:15: 9000000 INFO @ Tue, 16 Jun 2020 09:02:16: 3000000 INFO @ Tue, 16 Jun 2020 09:02:20: 10000000 INFO @ Tue, 16 Jun 2020 09:02:21: 4000000 INFO @ Tue, 16 Jun 2020 09:02:24: 11000000 INFO @ Tue, 16 Jun 2020 09:02:26: 5000000 INFO @ Tue, 16 Jun 2020 09:02:29: 12000000 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 09:02:31: 6000000 INFO @ Tue, 16 Jun 2020 09:02:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085410/SRX4085410.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085410/SRX4085410.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085410/SRX4085410.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085410/SRX4085410.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 09:02:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:02:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:02:34: 13000000 INFO @ Tue, 16 Jun 2020 09:02:35: 7000000 INFO @ Tue, 16 Jun 2020 09:02:37: 1000000 INFO @ Tue, 16 Jun 2020 09:02:39: 14000000 INFO @ Tue, 16 Jun 2020 09:02:40: 8000000 INFO @ Tue, 16 Jun 2020 09:02:42: 2000000 INFO @ Tue, 16 Jun 2020 09:02:44: 15000000 INFO @ Tue, 16 Jun 2020 09:02:45: 9000000 INFO @ Tue, 16 Jun 2020 09:02:47: 3000000 INFO @ Tue, 16 Jun 2020 09:02:48: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:02:48: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:02:48: #1 total tags in treatment: 4957404 INFO @ Tue, 16 Jun 2020 09:02:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:02:48: #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 09:02:48: #1 tags after filtering in treatment: 4332275 INFO @ Tue, 16 Jun 2020 09:02:48: #1 Redundant rate of treatment: 0.13 INFO @ Tue, 16 Jun 2020 09:02:48: #1 finished! INFO @ Tue, 16 Jun 2020 09:02:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:02:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:02:48: #2 number of paired peaks: 517 WARNING @ Tue, 16 Jun 2020 09:02:48: Fewer paired peaks (517) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 517 pairs to build model! INFO @ Tue, 16 Jun 2020 09:02:48: start model_add_line... INFO @ Tue, 16 Jun 2020 09:02:48: start X-correlation... INFO @ Tue, 16 Jun 2020 09:02:48: end of X-cor INFO @ Tue, 16 Jun 2020 09:02:48: #2 finished! INFO @ Tue, 16 Jun 2020 09:02:48: #2 predicted fragment length is 93 bps INFO @ Tue, 16 Jun 2020 09:02:48: #2 alternative fragment length(s) may be 93 bps INFO @ Tue, 16 Jun 2020 09:02:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085410/SRX4085410.05_model.r WARNING @ Tue, 16 Jun 2020 09:02:48: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:02:48: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Tue, 16 Jun 2020 09:02:48: #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 09:02:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:02:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:02:50: 10000000 INFO @ Tue, 16 Jun 2020 09:02:52: 4000000 INFO @ Tue, 16 Jun 2020 09:02:54: 11000000 INFO @ Tue, 16 Jun 2020 09:02:56: 5000000 INFO @ Tue, 16 Jun 2020 09:02:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:02:59: 12000000 INFO @ Tue, 16 Jun 2020 09:03:01: 6000000 INFO @ Tue, 16 Jun 2020 09:03:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085410/SRX4085410.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:03:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085410/SRX4085410.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:03:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085410/SRX4085410.05_summits.bed INFO @ Tue, 16 Jun 2020 09:03:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2242 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:03:04: 13000000 INFO @ Tue, 16 Jun 2020 09:03:06: 7000000 INFO @ Tue, 16 Jun 2020 09:03:09: 14000000 INFO @ Tue, 16 Jun 2020 09:03:11: 8000000 INFO @ Tue, 16 Jun 2020 09:03:13: 15000000 INFO @ Tue, 16 Jun 2020 09:03:16: 9000000 INFO @ Tue, 16 Jun 2020 09:03:17: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:03:17: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:03:17: #1 total tags in treatment: 4957404 INFO @ Tue, 16 Jun 2020 09:03:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:03:17: #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 09:03:17: #1 tags after filtering in treatment: 4332275 INFO @ Tue, 16 Jun 2020 09:03:17: #1 Redundant rate of treatment: 0.13 INFO @ Tue, 16 Jun 2020 09:03:17: #1 finished! INFO @ Tue, 16 Jun 2020 09:03:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:03:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:03:17: #2 number of paired peaks: 517 WARNING @ Tue, 16 Jun 2020 09:03:17: Fewer paired peaks (517) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 517 pairs to build model! INFO @ Tue, 16 Jun 2020 09:03:17: start model_add_line... INFO @ Tue, 16 Jun 2020 09:03:18: start X-correlation... INFO @ Tue, 16 Jun 2020 09:03:18: end of X-cor INFO @ Tue, 16 Jun 2020 09:03:18: #2 finished! INFO @ Tue, 16 Jun 2020 09:03:18: #2 predicted fragment length is 93 bps INFO @ Tue, 16 Jun 2020 09:03:18: #2 alternative fragment length(s) may be 93 bps INFO @ Tue, 16 Jun 2020 09:03:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085410/SRX4085410.10_model.r WARNING @ Tue, 16 Jun 2020 09:03:18: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:03:18: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Tue, 16 Jun 2020 09:03:18: #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 09:03:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:03:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:03:21: 10000000 INFO @ Tue, 16 Jun 2020 09:03:25: 11000000 INFO @ Tue, 16 Jun 2020 09:03:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:03:30: 12000000 INFO @ Tue, 16 Jun 2020 09:03:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085410/SRX4085410.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:03:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085410/SRX4085410.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:03:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085410/SRX4085410.10_summits.bed INFO @ Tue, 16 Jun 2020 09:03:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1213 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:03:35: 13000000 INFO @ Tue, 16 Jun 2020 09:03:40: 14000000 INFO @ Tue, 16 Jun 2020 09:03:44: 15000000 INFO @ Tue, 16 Jun 2020 09:03:48: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:03:48: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:03:48: #1 total tags in treatment: 4957404 INFO @ Tue, 16 Jun 2020 09:03:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:03:48: #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 09:03:48: #1 tags after filtering in treatment: 4332275 INFO @ Tue, 16 Jun 2020 09:03:48: #1 Redundant rate of treatment: 0.13 INFO @ Tue, 16 Jun 2020 09:03:48: #1 finished! INFO @ Tue, 16 Jun 2020 09:03:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:03:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:03:48: #2 number of paired peaks: 517 WARNING @ Tue, 16 Jun 2020 09:03:48: Fewer paired peaks (517) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 517 pairs to build model! INFO @ Tue, 16 Jun 2020 09:03:48: start model_add_line... INFO @ Tue, 16 Jun 2020 09:03:48: start X-correlation... INFO @ Tue, 16 Jun 2020 09:03:48: end of X-cor INFO @ Tue, 16 Jun 2020 09:03:48: #2 finished! INFO @ Tue, 16 Jun 2020 09:03:48: #2 predicted fragment length is 93 bps INFO @ Tue, 16 Jun 2020 09:03:48: #2 alternative fragment length(s) may be 93 bps INFO @ Tue, 16 Jun 2020 09:03:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085410/SRX4085410.20_model.r WARNING @ Tue, 16 Jun 2020 09:03:48: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:03:48: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Tue, 16 Jun 2020 09:03:48: #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 09:03:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:03:48: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:03:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:04:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085410/SRX4085410.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:04:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085410/SRX4085410.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:04:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085410/SRX4085410.20_summits.bed INFO @ Tue, 16 Jun 2020 09:04:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (461 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。