Job ID = 6367873 SRX = SRX4085440 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:42:44 prefetch.2.10.7: 1) Downloading 'SRR7167469'... 2020-06-15T23:42:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:51:05 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:51:05 prefetch.2.10.7: 1) 'SRR7167469' was downloaded successfully Read 26010822 spots for SRR7167469/SRR7167469.sra Written 26010822 spots for SRR7167469/SRR7167469.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: 00:18:34 26010822 reads; of these: 26010822 (100.00%) were paired; of these: 8306282 (31.93%) aligned concordantly 0 times 14689247 (56.47%) aligned concordantly exactly 1 time 3015293 (11.59%) aligned concordantly >1 times ---- 8306282 pairs aligned concordantly 0 times; of these: 390891 (4.71%) aligned discordantly 1 time ---- 7915391 pairs aligned 0 times concordantly or discordantly; of these: 15830782 mates make up the pairs; of these: 12483482 (78.86%) aligned 0 times 2872918 (18.15%) aligned exactly 1 time 474382 (3.00%) aligned >1 times 76.00% overall alignment rate Time searching: 00:18:35 Overall time: 00:18:35 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] 2338659 / 17970578 = 0.1301 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 09:23:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085440/SRX4085440.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085440/SRX4085440.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085440/SRX4085440.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085440/SRX4085440.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 09:23:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:23:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:23:23: 1000000 INFO @ Tue, 16 Jun 2020 09:23:28: 2000000 INFO @ Tue, 16 Jun 2020 09:23:34: 3000000 INFO @ Tue, 16 Jun 2020 09:23:40: 4000000 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 09:23:45: 5000000 INFO @ Tue, 16 Jun 2020 09:23:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085440/SRX4085440.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085440/SRX4085440.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085440/SRX4085440.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085440/SRX4085440.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 09:23:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:23:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:23:51: 6000000 INFO @ Tue, 16 Jun 2020 09:23:52: 1000000 INFO @ Tue, 16 Jun 2020 09:23:56: 7000000 INFO @ Tue, 16 Jun 2020 09:23:58: 2000000 INFO @ Tue, 16 Jun 2020 09:24:02: 8000000 INFO @ Tue, 16 Jun 2020 09:24:03: 3000000 INFO @ Tue, 16 Jun 2020 09:24:07: 9000000 INFO @ Tue, 16 Jun 2020 09:24:08: 4000000 INFO @ Tue, 16 Jun 2020 09:24:13: 10000000 INFO @ Tue, 16 Jun 2020 09:24:14: 5000000 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 09:24:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085440/SRX4085440.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085440/SRX4085440.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085440/SRX4085440.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085440/SRX4085440.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 09:24:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:24:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:24:19: 11000000 INFO @ Tue, 16 Jun 2020 09:24:19: 6000000 INFO @ Tue, 16 Jun 2020 09:24:23: 1000000 INFO @ Tue, 16 Jun 2020 09:24:24: 12000000 INFO @ Tue, 16 Jun 2020 09:24:24: 7000000 INFO @ Tue, 16 Jun 2020 09:24:28: 2000000 INFO @ Tue, 16 Jun 2020 09:24:30: 8000000 INFO @ Tue, 16 Jun 2020 09:24:30: 13000000 INFO @ Tue, 16 Jun 2020 09:24:34: 3000000 INFO @ Tue, 16 Jun 2020 09:24:35: 9000000 INFO @ Tue, 16 Jun 2020 09:24:35: 14000000 INFO @ Tue, 16 Jun 2020 09:24:40: 4000000 INFO @ Tue, 16 Jun 2020 09:24:40: 10000000 INFO @ Tue, 16 Jun 2020 09:24:41: 15000000 INFO @ Tue, 16 Jun 2020 09:24:45: 11000000 INFO @ Tue, 16 Jun 2020 09:24:45: 5000000 INFO @ Tue, 16 Jun 2020 09:24:47: 16000000 INFO @ Tue, 16 Jun 2020 09:24:50: 12000000 INFO @ Tue, 16 Jun 2020 09:24:51: 6000000 INFO @ Tue, 16 Jun 2020 09:24:52: 17000000 INFO @ Tue, 16 Jun 2020 09:24:55: 13000000 INFO @ Tue, 16 Jun 2020 09:24:56: 7000000 INFO @ Tue, 16 Jun 2020 09:24:58: 18000000 INFO @ Tue, 16 Jun 2020 09:25:00: 14000000 INFO @ Tue, 16 Jun 2020 09:25:02: 8000000 INFO @ Tue, 16 Jun 2020 09:25:03: 19000000 INFO @ Tue, 16 Jun 2020 09:25:06: 15000000 INFO @ Tue, 16 Jun 2020 09:25:07: 9000000 INFO @ Tue, 16 Jun 2020 09:25:09: 20000000 INFO @ Tue, 16 Jun 2020 09:25:11: 16000000 INFO @ Tue, 16 Jun 2020 09:25:13: 10000000 INFO @ Tue, 16 Jun 2020 09:25:15: 21000000 INFO @ Tue, 16 Jun 2020 09:25:16: 17000000 INFO @ Tue, 16 Jun 2020 09:25:19: 11000000 INFO @ Tue, 16 Jun 2020 09:25:21: 18000000 INFO @ Tue, 16 Jun 2020 09:25:21: 22000000 INFO @ Tue, 16 Jun 2020 09:25:25: 12000000 INFO @ Tue, 16 Jun 2020 09:25:26: 19000000 INFO @ Tue, 16 Jun 2020 09:25:27: 23000000 INFO @ Tue, 16 Jun 2020 09:25:30: 13000000 INFO @ Tue, 16 Jun 2020 09:25:31: 20000000 INFO @ Tue, 16 Jun 2020 09:25:33: 24000000 INFO @ Tue, 16 Jun 2020 09:25:36: 14000000 INFO @ Tue, 16 Jun 2020 09:25:36: 21000000 INFO @ Tue, 16 Jun 2020 09:25:39: 25000000 INFO @ Tue, 16 Jun 2020 09:25:41: 22000000 INFO @ Tue, 16 Jun 2020 09:25:42: 15000000 INFO @ Tue, 16 Jun 2020 09:25:45: 26000000 INFO @ Tue, 16 Jun 2020 09:25:47: 23000000 INFO @ Tue, 16 Jun 2020 09:25:48: 16000000 INFO @ Tue, 16 Jun 2020 09:25:51: 27000000 INFO @ Tue, 16 Jun 2020 09:25:52: 24000000 INFO @ Tue, 16 Jun 2020 09:25:54: 17000000 INFO @ Tue, 16 Jun 2020 09:25:57: 28000000 INFO @ Tue, 16 Jun 2020 09:25:57: 25000000 INFO @ Tue, 16 Jun 2020 09:26:00: 18000000 INFO @ Tue, 16 Jun 2020 09:26:02: 26000000 INFO @ Tue, 16 Jun 2020 09:26:03: 29000000 INFO @ Tue, 16 Jun 2020 09:26:05: 19000000 INFO @ Tue, 16 Jun 2020 09:26:07: 27000000 INFO @ Tue, 16 Jun 2020 09:26:09: 30000000 INFO @ Tue, 16 Jun 2020 09:26:11: 20000000 INFO @ Tue, 16 Jun 2020 09:26:13: 28000000 INFO @ Tue, 16 Jun 2020 09:26:14: 31000000 INFO @ Tue, 16 Jun 2020 09:26:17: 21000000 INFO @ Tue, 16 Jun 2020 09:26:18: 29000000 INFO @ Tue, 16 Jun 2020 09:26:20: 32000000 INFO @ Tue, 16 Jun 2020 09:26:22: 22000000 INFO @ Tue, 16 Jun 2020 09:26:23: 30000000 INFO @ Tue, 16 Jun 2020 09:26:26: 33000000 INFO @ Tue, 16 Jun 2020 09:26:28: 23000000 INFO @ Tue, 16 Jun 2020 09:26:28: 31000000 INFO @ Tue, 16 Jun 2020 09:26:31: 34000000 INFO @ Tue, 16 Jun 2020 09:26:33: 32000000 INFO @ Tue, 16 Jun 2020 09:26:34: 24000000 INFO @ Tue, 16 Jun 2020 09:26:36: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:26:36: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:26:36: #1 total tags in treatment: 15394508 INFO @ Tue, 16 Jun 2020 09:26:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:26:36: #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 09:26:36: #1 tags after filtering in treatment: 12521338 INFO @ Tue, 16 Jun 2020 09:26:36: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 16 Jun 2020 09:26:36: #1 finished! INFO @ Tue, 16 Jun 2020 09:26:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:26:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:26:37: #2 number of paired peaks: 261 WARNING @ Tue, 16 Jun 2020 09:26:37: Fewer paired peaks (261) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 261 pairs to build model! INFO @ Tue, 16 Jun 2020 09:26:37: start model_add_line... INFO @ Tue, 16 Jun 2020 09:26:37: start X-correlation... INFO @ Tue, 16 Jun 2020 09:26:37: end of X-cor INFO @ Tue, 16 Jun 2020 09:26:37: #2 finished! INFO @ Tue, 16 Jun 2020 09:26:37: #2 predicted fragment length is 91 bps INFO @ Tue, 16 Jun 2020 09:26:37: #2 alternative fragment length(s) may be 4,91 bps INFO @ Tue, 16 Jun 2020 09:26:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085440/SRX4085440.05_model.r WARNING @ Tue, 16 Jun 2020 09:26:37: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:26:37: #2 You may need to consider one of the other alternative d(s): 4,91 WARNING @ Tue, 16 Jun 2020 09:26:37: #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 09:26:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:26:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:26:38: 33000000 INFO @ Tue, 16 Jun 2020 09:26:39: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:26:43: 34000000 INFO @ Tue, 16 Jun 2020 09:26:45: 26000000 INFO @ Tue, 16 Jun 2020 09:26:48: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:26:48: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:26:48: #1 total tags in treatment: 15394508 INFO @ Tue, 16 Jun 2020 09:26:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:26:48: #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 09:26:48: #1 tags after filtering in treatment: 12521338 INFO @ Tue, 16 Jun 2020 09:26:48: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 16 Jun 2020 09:26:48: #1 finished! INFO @ Tue, 16 Jun 2020 09:26:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:26:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:26:49: #2 number of paired peaks: 261 WARNING @ Tue, 16 Jun 2020 09:26:49: Fewer paired peaks (261) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 261 pairs to build model! INFO @ Tue, 16 Jun 2020 09:26:49: start model_add_line... INFO @ Tue, 16 Jun 2020 09:26:49: start X-correlation... INFO @ Tue, 16 Jun 2020 09:26:49: end of X-cor INFO @ Tue, 16 Jun 2020 09:26:49: #2 finished! INFO @ Tue, 16 Jun 2020 09:26:49: #2 predicted fragment length is 91 bps INFO @ Tue, 16 Jun 2020 09:26:49: #2 alternative fragment length(s) may be 4,91 bps INFO @ Tue, 16 Jun 2020 09:26:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085440/SRX4085440.10_model.r WARNING @ Tue, 16 Jun 2020 09:26:49: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:26:49: #2 You may need to consider one of the other alternative d(s): 4,91 WARNING @ Tue, 16 Jun 2020 09:26:49: #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 09:26:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:26:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:26:50: 27000000 INFO @ Tue, 16 Jun 2020 09:26:57: 28000000 INFO @ Tue, 16 Jun 2020 09:27:02: 29000000 INFO @ Tue, 16 Jun 2020 09:27:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:27:08: 30000000 INFO @ Tue, 16 Jun 2020 09:27:14: 31000000 INFO @ Tue, 16 Jun 2020 09:27:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:27:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085440/SRX4085440.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:27:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085440/SRX4085440.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:27:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085440/SRX4085440.05_summits.bed INFO @ Tue, 16 Jun 2020 09:27:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4529 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:27:19: 32000000 INFO @ Tue, 16 Jun 2020 09:27:25: 33000000 INFO @ Tue, 16 Jun 2020 09:27:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085440/SRX4085440.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:27:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085440/SRX4085440.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:27:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085440/SRX4085440.10_summits.bed INFO @ Tue, 16 Jun 2020 09:27:28: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2393 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:27:30: 34000000 INFO @ Tue, 16 Jun 2020 09:27:35: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:27:35: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:27:35: #1 total tags in treatment: 15394508 INFO @ Tue, 16 Jun 2020 09:27:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:27:35: #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 09:27:35: #1 tags after filtering in treatment: 12521338 INFO @ Tue, 16 Jun 2020 09:27:35: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 16 Jun 2020 09:27:35: #1 finished! INFO @ Tue, 16 Jun 2020 09:27:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:27:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:27:36: #2 number of paired peaks: 261 WARNING @ Tue, 16 Jun 2020 09:27:36: Fewer paired peaks (261) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 261 pairs to build model! INFO @ Tue, 16 Jun 2020 09:27:36: start model_add_line... INFO @ Tue, 16 Jun 2020 09:27:36: start X-correlation... INFO @ Tue, 16 Jun 2020 09:27:36: end of X-cor INFO @ Tue, 16 Jun 2020 09:27:36: #2 finished! INFO @ Tue, 16 Jun 2020 09:27:36: #2 predicted fragment length is 91 bps INFO @ Tue, 16 Jun 2020 09:27:36: #2 alternative fragment length(s) may be 4,91 bps INFO @ Tue, 16 Jun 2020 09:27:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085440/SRX4085440.20_model.r WARNING @ Tue, 16 Jun 2020 09:27:36: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:27:36: #2 You may need to consider one of the other alternative d(s): 4,91 WARNING @ Tue, 16 Jun 2020 09:27:36: #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 09:27:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:27:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:28:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:28:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085440/SRX4085440.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:28:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085440/SRX4085440.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:28:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085440/SRX4085440.20_summits.bed INFO @ Tue, 16 Jun 2020 09:28:16: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (762 records, 4 fields): 2 millis CompletedMACS2peakCalling