Job ID = 6367238 SRX = SRX3058058 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:22:01 prefetch.2.10.7: 1) Downloading 'SRR5892349'... 2020-06-15T23:22:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:28:00 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:28:00 prefetch.2.10.7: 1) 'SRR5892349' was downloaded successfully 2020-06-15T23:28:00 prefetch.2.10.7: 'SRR5892349' has 0 unresolved dependencies Read 17819829 spots for SRR5892349/SRR5892349.sra Written 17819829 spots for SRR5892349/SRR5892349.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: 00:28:04 17819829 reads; of these: 17819829 (100.00%) were paired; of these: 5062261 (28.41%) aligned concordantly 0 times 11168862 (62.68%) aligned concordantly exactly 1 time 1588706 (8.92%) aligned concordantly >1 times ---- 5062261 pairs aligned concordantly 0 times; of these: 138989 (2.75%) aligned discordantly 1 time ---- 4923272 pairs aligned 0 times concordantly or discordantly; of these: 9846544 mates make up the pairs; of these: 9611652 (97.61%) aligned 0 times 160251 (1.63%) aligned exactly 1 time 74641 (0.76%) aligned >1 times 73.03% overall alignment rate Time searching: 00:28:04 Overall time: 00:28:04 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 20 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] 6331706 / 12874632 = 0.4918 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 09:09:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3058058/SRX3058058.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3058058/SRX3058058.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3058058/SRX3058058.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3058058/SRX3058058.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 09:09:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:23: 1000000 INFO @ Tue, 16 Jun 2020 09:09:32: 2000000 INFO @ Tue, 16 Jun 2020 09:09:41: 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 @ Tue, 16 Jun 2020 09:09:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3058058/SRX3058058.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3058058/SRX3058058.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3058058/SRX3058058.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3058058/SRX3058058.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 09:09:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:50: 4000000 INFO @ Tue, 16 Jun 2020 09:09:54: 1000000 INFO @ Tue, 16 Jun 2020 09:10:00: 5000000 INFO @ Tue, 16 Jun 2020 09:10:03: 2000000 INFO @ Tue, 16 Jun 2020 09:10:09: 6000000 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 09:10:13: 3000000 INFO @ Tue, 16 Jun 2020 09:10:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3058058/SRX3058058.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3058058/SRX3058058.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3058058/SRX3058058.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3058058/SRX3058058.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 09:10:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:18: 7000000 INFO @ Tue, 16 Jun 2020 09:10:22: 4000000 INFO @ Tue, 16 Jun 2020 09:10:25: 1000000 INFO @ Tue, 16 Jun 2020 09:10:28: 8000000 INFO @ Tue, 16 Jun 2020 09:10:32: 5000000 INFO @ Tue, 16 Jun 2020 09:10:35: 2000000 INFO @ Tue, 16 Jun 2020 09:10:38: 9000000 INFO @ Tue, 16 Jun 2020 09:10:41: 6000000 INFO @ Tue, 16 Jun 2020 09:10:45: 3000000 INFO @ Tue, 16 Jun 2020 09:10:47: 10000000 INFO @ Tue, 16 Jun 2020 09:10:51: 7000000 INFO @ Tue, 16 Jun 2020 09:10:55: 4000000 INFO @ Tue, 16 Jun 2020 09:10:57: 11000000 INFO @ Tue, 16 Jun 2020 09:11:00: 8000000 INFO @ Tue, 16 Jun 2020 09:11:05: 5000000 INFO @ Tue, 16 Jun 2020 09:11:07: 12000000 INFO @ Tue, 16 Jun 2020 09:11:09: 9000000 INFO @ Tue, 16 Jun 2020 09:11:15: 6000000 INFO @ Tue, 16 Jun 2020 09:11:16: 13000000 INFO @ Tue, 16 Jun 2020 09:11:19: 10000000 INFO @ Tue, 16 Jun 2020 09:11:20: #1 tag size is determined as 150 bps INFO @ Tue, 16 Jun 2020 09:11:20: #1 tag size = 150 INFO @ Tue, 16 Jun 2020 09:11:20: #1 total tags in treatment: 6462018 INFO @ Tue, 16 Jun 2020 09:11:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:11:20: #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 09:11:20: #1 tags after filtering in treatment: 6068435 INFO @ Tue, 16 Jun 2020 09:11:20: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 16 Jun 2020 09:11:20: #1 finished! INFO @ Tue, 16 Jun 2020 09:11:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:11:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:11:20: #2 number of paired peaks: 490 WARNING @ Tue, 16 Jun 2020 09:11:20: Fewer paired peaks (490) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 490 pairs to build model! INFO @ Tue, 16 Jun 2020 09:11:20: start model_add_line... INFO @ Tue, 16 Jun 2020 09:11:20: start X-correlation... INFO @ Tue, 16 Jun 2020 09:11:20: end of X-cor INFO @ Tue, 16 Jun 2020 09:11:20: #2 finished! INFO @ Tue, 16 Jun 2020 09:11:20: #2 predicted fragment length is 216 bps INFO @ Tue, 16 Jun 2020 09:11:20: #2 alternative fragment length(s) may be 216 bps INFO @ Tue, 16 Jun 2020 09:11:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3058058/SRX3058058.05_model.r WARNING @ Tue, 16 Jun 2020 09:11:20: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:11:20: #2 You may need to consider one of the other alternative d(s): 216 WARNING @ Tue, 16 Jun 2020 09:11:20: #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 09:11:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:11:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:11:25: 7000000 INFO @ Tue, 16 Jun 2020 09:11:28: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:11:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:11:35: 8000000 INFO @ Tue, 16 Jun 2020 09:11:38: 12000000 INFO @ Tue, 16 Jun 2020 09:11:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3058058/SRX3058058.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:11:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3058058/SRX3058058.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:11:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3058058/SRX3058058.05_summits.bed INFO @ Tue, 16 Jun 2020 09:11:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3135 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:11:44: 9000000 INFO @ Tue, 16 Jun 2020 09:11:47: 13000000 INFO @ Tue, 16 Jun 2020 09:11:50: #1 tag size is determined as 150 bps INFO @ Tue, 16 Jun 2020 09:11:50: #1 tag size = 150 INFO @ Tue, 16 Jun 2020 09:11:50: #1 total tags in treatment: 6462018 INFO @ Tue, 16 Jun 2020 09:11:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:11:50: #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 09:11:50: #1 tags after filtering in treatment: 6068435 INFO @ Tue, 16 Jun 2020 09:11:50: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 16 Jun 2020 09:11:50: #1 finished! INFO @ Tue, 16 Jun 2020 09:11:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:11:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:11:51: #2 number of paired peaks: 490 WARNING @ Tue, 16 Jun 2020 09:11:51: Fewer paired peaks (490) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 490 pairs to build model! INFO @ Tue, 16 Jun 2020 09:11:51: start model_add_line... INFO @ Tue, 16 Jun 2020 09:11:51: start X-correlation... INFO @ Tue, 16 Jun 2020 09:11:51: end of X-cor INFO @ Tue, 16 Jun 2020 09:11:51: #2 finished! INFO @ Tue, 16 Jun 2020 09:11:51: #2 predicted fragment length is 216 bps INFO @ Tue, 16 Jun 2020 09:11:51: #2 alternative fragment length(s) may be 216 bps INFO @ Tue, 16 Jun 2020 09:11:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3058058/SRX3058058.10_model.r WARNING @ Tue, 16 Jun 2020 09:11:51: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:11:51: #2 You may need to consider one of the other alternative d(s): 216 WARNING @ Tue, 16 Jun 2020 09:11:51: #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 09:11:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:11:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:11:54: 10000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:12:03: 11000000 INFO @ Tue, 16 Jun 2020 09:12:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:12: 12000000 INFO @ Tue, 16 Jun 2020 09:12:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3058058/SRX3058058.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3058058/SRX3058058.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3058058/SRX3058058.10_summits.bed INFO @ Tue, 16 Jun 2020 09:12:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1793 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:12:20: 13000000 INFO @ Tue, 16 Jun 2020 09:12:24: #1 tag size is determined as 150 bps INFO @ Tue, 16 Jun 2020 09:12:24: #1 tag size = 150 INFO @ Tue, 16 Jun 2020 09:12:24: #1 total tags in treatment: 6462018 INFO @ Tue, 16 Jun 2020 09:12:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:24: #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 09:12:24: #1 tags after filtering in treatment: 6068435 INFO @ Tue, 16 Jun 2020 09:12:24: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 16 Jun 2020 09:12:24: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:24: #2 number of paired peaks: 490 WARNING @ Tue, 16 Jun 2020 09:12:24: Fewer paired peaks (490) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 490 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:24: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:24: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:24: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:24: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:24: #2 predicted fragment length is 216 bps INFO @ Tue, 16 Jun 2020 09:12:24: #2 alternative fragment length(s) may be 216 bps INFO @ Tue, 16 Jun 2020 09:12:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3058058/SRX3058058.20_model.r WARNING @ Tue, 16 Jun 2020 09:12:24: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:12:24: #2 You may need to consider one of the other alternative d(s): 216 WARNING @ Tue, 16 Jun 2020 09:12:24: #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 09:12:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3058058/SRX3058058.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3058058/SRX3058058.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3058058/SRX3058058.20_summits.bed INFO @ Tue, 16 Jun 2020 09:12:46: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (749 records, 4 fields): 2 millis CompletedMACS2peakCalling