Job ID = 6367668 SRX = SRX3733162 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:35:05 prefetch.2.10.7: 1) Downloading 'SRR6760675'... 2020-06-15T23:35:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:47:42 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:47:43 prefetch.2.10.7: 1) 'SRR6760675' was downloaded successfully 2020-06-15T23:47:43 prefetch.2.10.7: 'SRR6760675' has 0 unresolved dependencies Read 32895075 spots for SRR6760675/SRR6760675.sra Written 32895075 spots for SRR6760675/SRR6760675.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: 00:41:31 32895075 reads; of these: 32895075 (100.00%) were paired; of these: 3217285 (9.78%) aligned concordantly 0 times 26405162 (80.27%) aligned concordantly exactly 1 time 3272628 (9.95%) aligned concordantly >1 times ---- 3217285 pairs aligned concordantly 0 times; of these: 1058892 (32.91%) aligned discordantly 1 time ---- 2158393 pairs aligned 0 times concordantly or discordantly; of these: 4316786 mates make up the pairs; of these: 3108256 (72.00%) aligned 0 times 747561 (17.32%) aligned exactly 1 time 460969 (10.68%) aligned >1 times 95.28% overall alignment rate Time searching: 00:41:31 Overall time: 00:41:31 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] 13733253 / 30432995 = 0.4513 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 09:49:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3733162/SRX3733162.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3733162/SRX3733162.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3733162/SRX3733162.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3733162/SRX3733162.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 09:49:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:49:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:49:42: 1000000 INFO @ Tue, 16 Jun 2020 09:49:51: 2000000 INFO @ Tue, 16 Jun 2020 09:49:59: 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 09:50:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3733162/SRX3733162.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3733162/SRX3733162.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3733162/SRX3733162.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3733162/SRX3733162.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 09:50:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:50:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:50:08: 4000000 INFO @ Tue, 16 Jun 2020 09:50:11: 1000000 INFO @ Tue, 16 Jun 2020 09:50:18: 5000000 INFO @ Tue, 16 Jun 2020 09:50:19: 2000000 INFO @ Tue, 16 Jun 2020 09:50:27: 6000000 INFO @ Tue, 16 Jun 2020 09:50:28: 3000000 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 09:50:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3733162/SRX3733162.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3733162/SRX3733162.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3733162/SRX3733162.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3733162/SRX3733162.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 09:50:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:50:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:50:37: 7000000 INFO @ Tue, 16 Jun 2020 09:50:37: 4000000 INFO @ Tue, 16 Jun 2020 09:50:42: 1000000 INFO @ Tue, 16 Jun 2020 09:50:46: 8000000 INFO @ Tue, 16 Jun 2020 09:50:46: 5000000 INFO @ Tue, 16 Jun 2020 09:50:51: 2000000 INFO @ Tue, 16 Jun 2020 09:50:56: 9000000 INFO @ Tue, 16 Jun 2020 09:50:56: 6000000 INFO @ Tue, 16 Jun 2020 09:51:00: 3000000 INFO @ Tue, 16 Jun 2020 09:51:05: 7000000 INFO @ Tue, 16 Jun 2020 09:51:06: 10000000 INFO @ Tue, 16 Jun 2020 09:51:10: 4000000 INFO @ Tue, 16 Jun 2020 09:51:14: 8000000 INFO @ Tue, 16 Jun 2020 09:51:15: 11000000 INFO @ Tue, 16 Jun 2020 09:51:19: 5000000 INFO @ Tue, 16 Jun 2020 09:51:23: 9000000 INFO @ Tue, 16 Jun 2020 09:51:25: 12000000 INFO @ Tue, 16 Jun 2020 09:51:28: 6000000 INFO @ Tue, 16 Jun 2020 09:51:32: 10000000 INFO @ Tue, 16 Jun 2020 09:51:35: 13000000 INFO @ Tue, 16 Jun 2020 09:51:37: 7000000 INFO @ Tue, 16 Jun 2020 09:51:41: 11000000 INFO @ Tue, 16 Jun 2020 09:51:45: 8000000 INFO @ Tue, 16 Jun 2020 09:51:45: 14000000 INFO @ Tue, 16 Jun 2020 09:51:50: 12000000 INFO @ Tue, 16 Jun 2020 09:51:54: 9000000 INFO @ Tue, 16 Jun 2020 09:51:55: 15000000 INFO @ Tue, 16 Jun 2020 09:51:58: 13000000 INFO @ Tue, 16 Jun 2020 09:52:02: 10000000 INFO @ Tue, 16 Jun 2020 09:52:04: 16000000 INFO @ Tue, 16 Jun 2020 09:52:07: 14000000 INFO @ Tue, 16 Jun 2020 09:52:11: 11000000 INFO @ Tue, 16 Jun 2020 09:52:14: 17000000 INFO @ Tue, 16 Jun 2020 09:52:16: 15000000 INFO @ Tue, 16 Jun 2020 09:52:19: 12000000 INFO @ Tue, 16 Jun 2020 09:52:23: 18000000 INFO @ Tue, 16 Jun 2020 09:52:25: 16000000 INFO @ Tue, 16 Jun 2020 09:52:28: 13000000 INFO @ Tue, 16 Jun 2020 09:52:32: 19000000 INFO @ Tue, 16 Jun 2020 09:52:33: 17000000 INFO @ Tue, 16 Jun 2020 09:52:37: 14000000 INFO @ Tue, 16 Jun 2020 09:52:42: 20000000 INFO @ Tue, 16 Jun 2020 09:52:42: 18000000 INFO @ Tue, 16 Jun 2020 09:52:46: 15000000 INFO @ Tue, 16 Jun 2020 09:52:51: 19000000 INFO @ Tue, 16 Jun 2020 09:52:51: 21000000 INFO @ Tue, 16 Jun 2020 09:52:54: 16000000 INFO @ Tue, 16 Jun 2020 09:52:59: 20000000 INFO @ Tue, 16 Jun 2020 09:53:00: 22000000 INFO @ Tue, 16 Jun 2020 09:53:03: 17000000 INFO @ Tue, 16 Jun 2020 09:53:08: 21000000 INFO @ Tue, 16 Jun 2020 09:53:10: 23000000 INFO @ Tue, 16 Jun 2020 09:53:12: 18000000 INFO @ Tue, 16 Jun 2020 09:53:17: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:53:19: 24000000 INFO @ Tue, 16 Jun 2020 09:53:20: 19000000 INFO @ Tue, 16 Jun 2020 09:53:25: 23000000 INFO @ Tue, 16 Jun 2020 09:53:28: 25000000 INFO @ Tue, 16 Jun 2020 09:53:29: 20000000 INFO @ Tue, 16 Jun 2020 09:53:34: 24000000 INFO @ Tue, 16 Jun 2020 09:53:37: 21000000 INFO @ Tue, 16 Jun 2020 09:53:38: 26000000 INFO @ Tue, 16 Jun 2020 09:53:42: 25000000 INFO @ Tue, 16 Jun 2020 09:53:46: 22000000 INFO @ Tue, 16 Jun 2020 09:53:47: 27000000 INFO @ Tue, 16 Jun 2020 09:53:51: 26000000 INFO @ Tue, 16 Jun 2020 09:53:54: 23000000 INFO @ Tue, 16 Jun 2020 09:53:56: 28000000 INFO @ Tue, 16 Jun 2020 09:53:59: 27000000 INFO @ Tue, 16 Jun 2020 09:54:03: 24000000 INFO @ Tue, 16 Jun 2020 09:54:05: 29000000 INFO @ Tue, 16 Jun 2020 09:54:08: 28000000 INFO @ Tue, 16 Jun 2020 09:54:12: 25000000 INFO @ Tue, 16 Jun 2020 09:54:15: 30000000 INFO @ Tue, 16 Jun 2020 09:54:16: 29000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:54:20: 26000000 INFO @ Tue, 16 Jun 2020 09:54:24: 31000000 INFO @ Tue, 16 Jun 2020 09:54:25: 30000000 INFO @ Tue, 16 Jun 2020 09:54:29: 27000000 INFO @ Tue, 16 Jun 2020 09:54:33: 31000000 INFO @ Tue, 16 Jun 2020 09:54:34: 32000000 INFO @ Tue, 16 Jun 2020 09:54:37: 28000000 INFO @ Tue, 16 Jun 2020 09:54:42: 32000000 INFO @ Tue, 16 Jun 2020 09:54:43: 33000000 INFO @ Tue, 16 Jun 2020 09:54:46: 29000000 INFO @ Tue, 16 Jun 2020 09:54:51: 33000000 INFO @ Tue, 16 Jun 2020 09:54:52: 34000000 INFO @ Tue, 16 Jun 2020 09:54:54: 30000000 INFO @ Tue, 16 Jun 2020 09:54:59: 34000000 INFO @ Tue, 16 Jun 2020 09:55:01: 35000000 INFO @ Tue, 16 Jun 2020 09:55:03: 31000000 INFO @ Tue, 16 Jun 2020 09:55:03: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:55:03: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:55:03: #1 total tags in treatment: 16209138 INFO @ Tue, 16 Jun 2020 09:55:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:55:03: #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 09:55:03: #1 tags after filtering in treatment: 13937952 INFO @ Tue, 16 Jun 2020 09:55:03: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 16 Jun 2020 09:55:03: #1 finished! INFO @ Tue, 16 Jun 2020 09:55:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:55:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:55:04: #2 number of paired peaks: 371 WARNING @ Tue, 16 Jun 2020 09:55:04: Fewer paired peaks (371) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 371 pairs to build model! INFO @ Tue, 16 Jun 2020 09:55:04: start model_add_line... INFO @ Tue, 16 Jun 2020 09:55:04: start X-correlation... INFO @ Tue, 16 Jun 2020 09:55:05: end of X-cor INFO @ Tue, 16 Jun 2020 09:55:05: #2 finished! INFO @ Tue, 16 Jun 2020 09:55:05: #2 predicted fragment length is 141 bps INFO @ Tue, 16 Jun 2020 09:55:05: #2 alternative fragment length(s) may be 4,141,156,159,168 bps INFO @ Tue, 16 Jun 2020 09:55:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3733162/SRX3733162.05_model.r WARNING @ Tue, 16 Jun 2020 09:55:05: #2 Since the d (141) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:55:05: #2 You may need to consider one of the other alternative d(s): 4,141,156,159,168 WARNING @ Tue, 16 Jun 2020 09:55:05: #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 09:55:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:55:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:55:08: 35000000 INFO @ Tue, 16 Jun 2020 09:55:10: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:55:10: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:55:10: #1 total tags in treatment: 16209138 INFO @ Tue, 16 Jun 2020 09:55:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:55:10: #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 09:55:10: #1 tags after filtering in treatment: 13937952 INFO @ Tue, 16 Jun 2020 09:55:10: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 16 Jun 2020 09:55:10: #1 finished! INFO @ Tue, 16 Jun 2020 09:55:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:55:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:55:11: 32000000 INFO @ Tue, 16 Jun 2020 09:55:11: #2 number of paired peaks: 371 WARNING @ Tue, 16 Jun 2020 09:55:11: Fewer paired peaks (371) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 371 pairs to build model! INFO @ Tue, 16 Jun 2020 09:55:11: start model_add_line... INFO @ Tue, 16 Jun 2020 09:55:11: start X-correlation... INFO @ Tue, 16 Jun 2020 09:55:11: end of X-cor INFO @ Tue, 16 Jun 2020 09:55:11: #2 finished! INFO @ Tue, 16 Jun 2020 09:55:11: #2 predicted fragment length is 141 bps INFO @ Tue, 16 Jun 2020 09:55:11: #2 alternative fragment length(s) may be 4,141,156,159,168 bps INFO @ Tue, 16 Jun 2020 09:55:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3733162/SRX3733162.10_model.r WARNING @ Tue, 16 Jun 2020 09:55:11: #2 Since the d (141) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:55:11: #2 You may need to consider one of the other alternative d(s): 4,141,156,159,168 WARNING @ Tue, 16 Jun 2020 09:55:11: #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 09:55:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:55:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:55:18: 33000000 INFO @ Tue, 16 Jun 2020 09:55:25: 34000000 INFO @ Tue, 16 Jun 2020 09:55:32: 35000000 INFO @ Tue, 16 Jun 2020 09:55:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:55:33: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:55:33: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:55:33: #1 total tags in treatment: 16209138 INFO @ Tue, 16 Jun 2020 09:55:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:55:33: #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 09:55:34: #1 tags after filtering in treatment: 13937952 INFO @ Tue, 16 Jun 2020 09:55:34: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 16 Jun 2020 09:55:34: #1 finished! INFO @ Tue, 16 Jun 2020 09:55:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:55:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:55:35: #2 number of paired peaks: 371 WARNING @ Tue, 16 Jun 2020 09:55:35: Fewer paired peaks (371) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 371 pairs to build model! INFO @ Tue, 16 Jun 2020 09:55:35: start model_add_line... INFO @ Tue, 16 Jun 2020 09:55:35: start X-correlation... INFO @ Tue, 16 Jun 2020 09:55:35: end of X-cor INFO @ Tue, 16 Jun 2020 09:55:35: #2 finished! INFO @ Tue, 16 Jun 2020 09:55:35: #2 predicted fragment length is 141 bps INFO @ Tue, 16 Jun 2020 09:55:35: #2 alternative fragment length(s) may be 4,141,156,159,168 bps INFO @ Tue, 16 Jun 2020 09:55:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3733162/SRX3733162.20_model.r WARNING @ Tue, 16 Jun 2020 09:55:35: #2 Since the d (141) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:55:35: #2 You may need to consider one of the other alternative d(s): 4,141,156,159,168 WARNING @ Tue, 16 Jun 2020 09:55:35: #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 09:55:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:55:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:55:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:55:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3733162/SRX3733162.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:55:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3733162/SRX3733162.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:55:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3733162/SRX3733162.05_summits.bed INFO @ Tue, 16 Jun 2020 09:55:46: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (543 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:55:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3733162/SRX3733162.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:55:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3733162/SRX3733162.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:55:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3733162/SRX3733162.10_summits.bed INFO @ Tue, 16 Jun 2020 09:55:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (387 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:56:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:56:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3733162/SRX3733162.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:56:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3733162/SRX3733162.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:56:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3733162/SRX3733162.20_summits.bed INFO @ Tue, 16 Jun 2020 09:56:15: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (240 records, 4 fields): 1 millis CompletedMACS2peakCalling