Job ID = 6368627 SRX = SRX5064643 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-16T00:18:06 prefetch.2.10.7: 1) Downloading 'SRR8246579'... 2020-06-16T00:18:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:24:24 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:24:24 prefetch.2.10.7: 1) 'SRR8246579' was downloaded successfully 2020-06-16T00:24:24 prefetch.2.10.7: 'SRR8246579' has 0 unresolved dependencies Read 18447129 spots for SRR8246579/SRR8246579.sra Written 18447129 spots for SRR8246579/SRR8246579.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: 00:46:05 18447129 reads; of these: 18447129 (100.00%) were paired; of these: 1009096 (5.47%) aligned concordantly 0 times 15284098 (82.85%) aligned concordantly exactly 1 time 2153935 (11.68%) aligned concordantly >1 times ---- 1009096 pairs aligned concordantly 0 times; of these: 358504 (35.53%) aligned discordantly 1 time ---- 650592 pairs aligned 0 times concordantly or discordantly; of these: 1301184 mates make up the pairs; of these: 979466 (75.27%) aligned 0 times 205260 (15.77%) aligned exactly 1 time 116458 (8.95%) aligned >1 times 97.35% overall alignment rate Time searching: 00:46:05 Overall time: 00:46:05 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 28 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] 4597181 / 17701158 = 0.2597 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 10:29:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5064643/SRX5064643.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5064643/SRX5064643.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5064643/SRX5064643.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5064643/SRX5064643.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 10:29:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:29:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:30:00: 1000000 INFO @ Tue, 16 Jun 2020 10:30:11: 2000000 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 10:30:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5064643/SRX5064643.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5064643/SRX5064643.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5064643/SRX5064643.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5064643/SRX5064643.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 10:30:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:30:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:30:23: 3000000 INFO @ Tue, 16 Jun 2020 10:30:32: 1000000 INFO @ Tue, 16 Jun 2020 10:30:37: 4000000 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 10:30:46: 2000000 INFO @ Tue, 16 Jun 2020 10:30:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5064643/SRX5064643.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5064643/SRX5064643.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5064643/SRX5064643.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5064643/SRX5064643.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 10:30:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:30:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:30:51: 5000000 INFO @ Tue, 16 Jun 2020 10:30:57: 1000000 INFO @ Tue, 16 Jun 2020 10:31:01: 3000000 INFO @ Tue, 16 Jun 2020 10:31:06: 2000000 INFO @ Tue, 16 Jun 2020 10:31:06: 6000000 INFO @ Tue, 16 Jun 2020 10:31:14: 3000000 INFO @ Tue, 16 Jun 2020 10:31:16: 4000000 INFO @ Tue, 16 Jun 2020 10:31:20: 7000000 INFO @ Tue, 16 Jun 2020 10:31:23: 4000000 INFO @ Tue, 16 Jun 2020 10:31:30: 5000000 INFO @ Tue, 16 Jun 2020 10:31:32: 5000000 INFO @ Tue, 16 Jun 2020 10:31:35: 8000000 INFO @ Tue, 16 Jun 2020 10:31:40: 6000000 INFO @ Tue, 16 Jun 2020 10:31:45: 6000000 INFO @ Tue, 16 Jun 2020 10:31:49: 7000000 INFO @ Tue, 16 Jun 2020 10:31:50: 9000000 INFO @ Tue, 16 Jun 2020 10:31:58: 8000000 INFO @ Tue, 16 Jun 2020 10:31:59: 7000000 INFO @ Tue, 16 Jun 2020 10:32:04: 10000000 INFO @ Tue, 16 Jun 2020 10:32:06: 9000000 INFO @ Tue, 16 Jun 2020 10:32:13: 8000000 INFO @ Tue, 16 Jun 2020 10:32:15: 10000000 INFO @ Tue, 16 Jun 2020 10:32:18: 11000000 INFO @ Tue, 16 Jun 2020 10:32:23: 11000000 INFO @ Tue, 16 Jun 2020 10:32:27: 9000000 INFO @ Tue, 16 Jun 2020 10:32:31: 12000000 INFO @ Tue, 16 Jun 2020 10:32:32: 12000000 INFO @ Tue, 16 Jun 2020 10:32:40: 10000000 INFO @ Tue, 16 Jun 2020 10:32:41: 13000000 INFO @ Tue, 16 Jun 2020 10:32:44: 13000000 INFO @ Tue, 16 Jun 2020 10:32:49: 14000000 INFO @ Tue, 16 Jun 2020 10:32:53: 11000000 INFO @ Tue, 16 Jun 2020 10:32:56: 14000000 INFO @ Tue, 16 Jun 2020 10:32:57: 15000000 INFO @ Tue, 16 Jun 2020 10:33:05: 12000000 INFO @ Tue, 16 Jun 2020 10:33:06: 16000000 INFO @ Tue, 16 Jun 2020 10:33:08: 15000000 INFO @ Tue, 16 Jun 2020 10:33:14: 17000000 INFO @ Tue, 16 Jun 2020 10:33:18: 13000000 INFO @ Tue, 16 Jun 2020 10:33:20: 16000000 INFO @ Tue, 16 Jun 2020 10:33:22: 18000000 INFO @ Tue, 16 Jun 2020 10:33:30: 14000000 INFO @ Tue, 16 Jun 2020 10:33:30: 19000000 INFO @ Tue, 16 Jun 2020 10:33:33: 17000000 INFO @ Tue, 16 Jun 2020 10:33:39: 20000000 INFO @ Tue, 16 Jun 2020 10:33:42: 15000000 INFO @ Tue, 16 Jun 2020 10:33:45: 18000000 INFO @ Tue, 16 Jun 2020 10:33:47: 21000000 INFO @ Tue, 16 Jun 2020 10:33:54: 16000000 INFO @ Tue, 16 Jun 2020 10:33:55: 22000000 INFO @ Tue, 16 Jun 2020 10:33:57: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:34:03: 23000000 INFO @ Tue, 16 Jun 2020 10:34:07: 17000000 INFO @ Tue, 16 Jun 2020 10:34:08: 20000000 INFO @ Tue, 16 Jun 2020 10:34:12: 24000000 INFO @ Tue, 16 Jun 2020 10:34:18: 18000000 INFO @ Tue, 16 Jun 2020 10:34:20: 25000000 INFO @ Tue, 16 Jun 2020 10:34:20: 21000000 INFO @ Tue, 16 Jun 2020 10:34:28: 26000000 INFO @ Tue, 16 Jun 2020 10:34:30: 19000000 INFO @ Tue, 16 Jun 2020 10:34:32: 22000000 INFO @ Tue, 16 Jun 2020 10:34:34: #1 tag size is determined as 150 bps INFO @ Tue, 16 Jun 2020 10:34:34: #1 tag size = 150 INFO @ Tue, 16 Jun 2020 10:34:34: #1 total tags in treatment: 12895179 INFO @ Tue, 16 Jun 2020 10:34:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:34:34: #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 10:34:34: #1 tags after filtering in treatment: 11901917 INFO @ Tue, 16 Jun 2020 10:34:34: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 16 Jun 2020 10:34:34: #1 finished! INFO @ Tue, 16 Jun 2020 10:34:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:34:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:34:35: #2 number of paired peaks: 337 WARNING @ Tue, 16 Jun 2020 10:34:35: Fewer paired peaks (337) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 337 pairs to build model! INFO @ Tue, 16 Jun 2020 10:34:35: start model_add_line... INFO @ Tue, 16 Jun 2020 10:34:35: start X-correlation... INFO @ Tue, 16 Jun 2020 10:34:35: end of X-cor INFO @ Tue, 16 Jun 2020 10:34:35: #2 finished! INFO @ Tue, 16 Jun 2020 10:34:35: #2 predicted fragment length is 217 bps INFO @ Tue, 16 Jun 2020 10:34:35: #2 alternative fragment length(s) may be 217 bps INFO @ Tue, 16 Jun 2020 10:34:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5064643/SRX5064643.20_model.r WARNING @ Tue, 16 Jun 2020 10:34:35: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:34:35: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Tue, 16 Jun 2020 10:34:35: #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 10:34:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:34:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:34:42: 20000000 INFO @ Tue, 16 Jun 2020 10:34:44: 23000000 INFO @ Tue, 16 Jun 2020 10:34:54: 21000000 INFO @ Tue, 16 Jun 2020 10:34:56: 24000000 INFO @ Tue, 16 Jun 2020 10:34:58: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:35:07: 22000000 INFO @ Tue, 16 Jun 2020 10:35:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5064643/SRX5064643.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:35:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5064643/SRX5064643.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:35:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5064643/SRX5064643.20_summits.bed INFO @ Tue, 16 Jun 2020 10:35:08: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (248 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:35:08: 25000000 INFO @ Tue, 16 Jun 2020 10:35:19: 23000000 INFO @ Tue, 16 Jun 2020 10:35:21: 26000000 INFO @ Tue, 16 Jun 2020 10:35:30: #1 tag size is determined as 150 bps INFO @ Tue, 16 Jun 2020 10:35:30: #1 tag size = 150 INFO @ Tue, 16 Jun 2020 10:35:30: #1 total tags in treatment: 12895179 INFO @ Tue, 16 Jun 2020 10:35:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:35:30: #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 10:35:30: #1 tags after filtering in treatment: 11901917 INFO @ Tue, 16 Jun 2020 10:35:30: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 16 Jun 2020 10:35:30: #1 finished! INFO @ Tue, 16 Jun 2020 10:35:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:35:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:35:31: #2 number of paired peaks: 337 WARNING @ Tue, 16 Jun 2020 10:35:31: Fewer paired peaks (337) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 337 pairs to build model! INFO @ Tue, 16 Jun 2020 10:35:31: start model_add_line... INFO @ Tue, 16 Jun 2020 10:35:31: start X-correlation... INFO @ Tue, 16 Jun 2020 10:35:31: end of X-cor INFO @ Tue, 16 Jun 2020 10:35:31: #2 finished! INFO @ Tue, 16 Jun 2020 10:35:31: #2 predicted fragment length is 217 bps INFO @ Tue, 16 Jun 2020 10:35:31: #2 alternative fragment length(s) may be 217 bps INFO @ Tue, 16 Jun 2020 10:35:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5064643/SRX5064643.05_model.r WARNING @ Tue, 16 Jun 2020 10:35:31: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:35:31: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Tue, 16 Jun 2020 10:35:31: #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 10:35:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:35:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:35:31: 24000000 INFO @ Tue, 16 Jun 2020 10:35:42: 25000000 INFO @ Tue, 16 Jun 2020 10:35:53: 26000000 INFO @ Tue, 16 Jun 2020 10:35:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:36:01: #1 tag size is determined as 150 bps INFO @ Tue, 16 Jun 2020 10:36:01: #1 tag size = 150 INFO @ Tue, 16 Jun 2020 10:36:01: #1 total tags in treatment: 12895179 INFO @ Tue, 16 Jun 2020 10:36:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:36:01: #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 10:36:01: #1 tags after filtering in treatment: 11901917 INFO @ Tue, 16 Jun 2020 10:36:01: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 16 Jun 2020 10:36:01: #1 finished! INFO @ Tue, 16 Jun 2020 10:36:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:36:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:36:02: #2 number of paired peaks: 337 WARNING @ Tue, 16 Jun 2020 10:36:02: Fewer paired peaks (337) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 337 pairs to build model! INFO @ Tue, 16 Jun 2020 10:36:02: start model_add_line... INFO @ Tue, 16 Jun 2020 10:36:02: start X-correlation... INFO @ Tue, 16 Jun 2020 10:36:02: end of X-cor INFO @ Tue, 16 Jun 2020 10:36:02: #2 finished! INFO @ Tue, 16 Jun 2020 10:36:02: #2 predicted fragment length is 217 bps INFO @ Tue, 16 Jun 2020 10:36:02: #2 alternative fragment length(s) may be 217 bps INFO @ Tue, 16 Jun 2020 10:36:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5064643/SRX5064643.10_model.r WARNING @ Tue, 16 Jun 2020 10:36:02: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:36:02: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Tue, 16 Jun 2020 10:36:02: #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 10:36:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:36:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:36:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5064643/SRX5064643.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:36:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5064643/SRX5064643.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:36:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5064643/SRX5064643.05_summits.bed INFO @ Tue, 16 Jun 2020 10:36:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (438 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:36:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:36:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5064643/SRX5064643.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:36:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5064643/SRX5064643.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:36:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5064643/SRX5064643.10_summits.bed INFO @ Tue, 16 Jun 2020 10:36:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (352 records, 4 fields): 1 millis CompletedMACS2peakCalling