Job ID = 5720198 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 25,253,342 reads read : 50,506,684 reads written : 50,506,684 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:10:19 25253342 reads; of these: 25253342 (100.00%) were paired; of these: 11845989 (46.91%) aligned concordantly 0 times 10485363 (41.52%) aligned concordantly exactly 1 time 2921990 (11.57%) aligned concordantly >1 times ---- 11845989 pairs aligned concordantly 0 times; of these: 6190502 (52.26%) aligned discordantly 1 time ---- 5655487 pairs aligned 0 times concordantly or discordantly; of these: 11310974 mates make up the pairs; of these: 8581446 (75.87%) aligned 0 times 977425 (8.64%) aligned exactly 1 time 1752103 (15.49%) aligned >1 times 83.01% overall alignment rate Time searching: 01:10:20 Overall time: 01:10:20 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 32 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] 2281245 / 19130648 = 0.1192 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 @ Wed, 15 Apr 2020 23:46:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6619567/SRX6619567.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6619567/SRX6619567.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6619567/SRX6619567.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6619567/SRX6619567.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 @ Wed, 15 Apr 2020 23:46:18: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:46:18: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:46:26: 1000000 INFO @ Wed, 15 Apr 2020 23:46:33: 2000000 INFO @ Wed, 15 Apr 2020 23:46:41: 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 @ Wed, 15 Apr 2020 23:46:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6619567/SRX6619567.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6619567/SRX6619567.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6619567/SRX6619567.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6619567/SRX6619567.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 @ Wed, 15 Apr 2020 23:46:47: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:46:47: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:46:47: 4000000 INFO @ Wed, 15 Apr 2020 23:46:55: 5000000 INFO @ Wed, 15 Apr 2020 23:46:55: 1000000 INFO @ Wed, 15 Apr 2020 23:47:01: 6000000 INFO @ Wed, 15 Apr 2020 23:47:02: 2000000 INFO @ Wed, 15 Apr 2020 23:47:08: 7000000 INFO @ Wed, 15 Apr 2020 23:47:09: 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 @ Wed, 15 Apr 2020 23:47:15: 8000000 INFO @ Wed, 15 Apr 2020 23:47:16: 4000000 INFO @ Wed, 15 Apr 2020 23:47:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6619567/SRX6619567.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6619567/SRX6619567.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6619567/SRX6619567.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6619567/SRX6619567.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 @ Wed, 15 Apr 2020 23:47:17: #1 read tag files... INFO @ Wed, 15 Apr 2020 23:47:17: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 23:47:22: 9000000 INFO @ Wed, 15 Apr 2020 23:47:24: 5000000 INFO @ Wed, 15 Apr 2020 23:47:25: 1000000 INFO @ Wed, 15 Apr 2020 23:47:29: 10000000 INFO @ Wed, 15 Apr 2020 23:47:31: 6000000 INFO @ Wed, 15 Apr 2020 23:47:33: 2000000 INFO @ Wed, 15 Apr 2020 23:47:36: 11000000 INFO @ Wed, 15 Apr 2020 23:47:39: 7000000 INFO @ Wed, 15 Apr 2020 23:47:40: 3000000 INFO @ Wed, 15 Apr 2020 23:47:44: 12000000 INFO @ Wed, 15 Apr 2020 23:47:47: 8000000 INFO @ Wed, 15 Apr 2020 23:47:48: 4000000 INFO @ Wed, 15 Apr 2020 23:47:51: 13000000 INFO @ Wed, 15 Apr 2020 23:47:54: 9000000 INFO @ Wed, 15 Apr 2020 23:47:56: 5000000 INFO @ Wed, 15 Apr 2020 23:47:58: 14000000 INFO @ Wed, 15 Apr 2020 23:48:02: 10000000 INFO @ Wed, 15 Apr 2020 23:48:03: 6000000 INFO @ Wed, 15 Apr 2020 23:48:04: 15000000 INFO @ Wed, 15 Apr 2020 23:48:09: 11000000 INFO @ Wed, 15 Apr 2020 23:48:11: 7000000 INFO @ Wed, 15 Apr 2020 23:48:11: 16000000 INFO @ Wed, 15 Apr 2020 23:48:17: 12000000 INFO @ Wed, 15 Apr 2020 23:48:18: 17000000 INFO @ Wed, 15 Apr 2020 23:48:18: 8000000 INFO @ Wed, 15 Apr 2020 23:48:25: 13000000 INFO @ Wed, 15 Apr 2020 23:48:25: 18000000 INFO @ Wed, 15 Apr 2020 23:48:26: 9000000 INFO @ Wed, 15 Apr 2020 23:48:32: 19000000 INFO @ Wed, 15 Apr 2020 23:48:33: 14000000 INFO @ Wed, 15 Apr 2020 23:48:34: 10000000 INFO @ Wed, 15 Apr 2020 23:48:39: 20000000 INFO @ Wed, 15 Apr 2020 23:48:41: 15000000 INFO @ Wed, 15 Apr 2020 23:48:42: 11000000 INFO @ Wed, 15 Apr 2020 23:48:46: 21000000 INFO @ Wed, 15 Apr 2020 23:48:49: 16000000 INFO @ Wed, 15 Apr 2020 23:48:49: 12000000 INFO @ Wed, 15 Apr 2020 23:48:53: 22000000 INFO @ Wed, 15 Apr 2020 23:48:57: 17000000 INFO @ Wed, 15 Apr 2020 23:48:57: 13000000 INFO @ Wed, 15 Apr 2020 23:49:00: 23000000 INFO @ Wed, 15 Apr 2020 23:49:04: 18000000 INFO @ Wed, 15 Apr 2020 23:49:04: 14000000 INFO @ Wed, 15 Apr 2020 23:49:07: 24000000 INFO @ Wed, 15 Apr 2020 23:49:12: 19000000 INFO @ Wed, 15 Apr 2020 23:49:12: 15000000 INFO @ Wed, 15 Apr 2020 23:49:14: 25000000 INFO @ Wed, 15 Apr 2020 23:49:19: 20000000 INFO @ Wed, 15 Apr 2020 23:49:20: 16000000 INFO @ Wed, 15 Apr 2020 23:49:21: 26000000 INFO @ Wed, 15 Apr 2020 23:49:27: 21000000 INFO @ Wed, 15 Apr 2020 23:49:27: 17000000 INFO @ Wed, 15 Apr 2020 23:49:28: 27000000 INFO @ Wed, 15 Apr 2020 23:49:34: 22000000 INFO @ Wed, 15 Apr 2020 23:49:35: 18000000 INFO @ Wed, 15 Apr 2020 23:49:35: 28000000 INFO @ Wed, 15 Apr 2020 23:49:42: 23000000 INFO @ Wed, 15 Apr 2020 23:49:42: 19000000 INFO @ Wed, 15 Apr 2020 23:49:42: 29000000 INFO @ Wed, 15 Apr 2020 23:49:49: 24000000 INFO @ Wed, 15 Apr 2020 23:49:49: 30000000 INFO @ Wed, 15 Apr 2020 23:49:49: 20000000 INFO @ Wed, 15 Apr 2020 23:49:56: 31000000 INFO @ Wed, 15 Apr 2020 23:49:57: 21000000 INFO @ Wed, 15 Apr 2020 23:49:57: 25000000 INFO @ Wed, 15 Apr 2020 23:50:03: 32000000 INFO @ Wed, 15 Apr 2020 23:50:04: 22000000 INFO @ Wed, 15 Apr 2020 23:50:05: 26000000 INFO @ Wed, 15 Apr 2020 23:50:10: 33000000 INFO @ Wed, 15 Apr 2020 23:50:12: 23000000 INFO @ Wed, 15 Apr 2020 23:50:13: 27000000 INFO @ Wed, 15 Apr 2020 23:50:17: 34000000 INFO @ Wed, 15 Apr 2020 23:50:19: 24000000 INFO @ Wed, 15 Apr 2020 23:50:20: 28000000 INFO @ Wed, 15 Apr 2020 23:50:24: 35000000 INFO @ Wed, 15 Apr 2020 23:50:27: 25000000 INFO @ Wed, 15 Apr 2020 23:50:28: 29000000 INFO @ Wed, 15 Apr 2020 23:50:31: 36000000 INFO @ Wed, 15 Apr 2020 23:50:35: 26000000 INFO @ Wed, 15 Apr 2020 23:50:36: 30000000 INFO @ Wed, 15 Apr 2020 23:50:38: 37000000 INFO @ Wed, 15 Apr 2020 23:50:41: #1 tag size is determined as 150 bps INFO @ Wed, 15 Apr 2020 23:50:41: #1 tag size = 150 INFO @ Wed, 15 Apr 2020 23:50:41: #1 total tags in treatment: 11657390 INFO @ Wed, 15 Apr 2020 23:50:41: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:50:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 23:50:41: #1 tags after filtering in treatment: 9680731 INFO @ Wed, 15 Apr 2020 23:50:41: #1 Redundant rate of treatment: 0.17 INFO @ Wed, 15 Apr 2020 23:50:41: #1 finished! INFO @ Wed, 15 Apr 2020 23:50:41: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:50:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:50:42: #2 number of paired peaks: 374 WARNING @ Wed, 15 Apr 2020 23:50:42: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Wed, 15 Apr 2020 23:50:42: start model_add_line... INFO @ Wed, 15 Apr 2020 23:50:42: start X-correlation... INFO @ Wed, 15 Apr 2020 23:50:42: end of X-cor INFO @ Wed, 15 Apr 2020 23:50:42: #2 finished! INFO @ Wed, 15 Apr 2020 23:50:42: #2 predicted fragment length is 199 bps INFO @ Wed, 15 Apr 2020 23:50:42: #2 alternative fragment length(s) may be 199,217 bps INFO @ Wed, 15 Apr 2020 23:50:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6619567/SRX6619567.05_model.r WARNING @ Wed, 15 Apr 2020 23:50:42: #2 Since the d (199) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 23:50:42: #2 You may need to consider one of the other alternative d(s): 199,217 WARNING @ Wed, 15 Apr 2020 23:50:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 23:50:42: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:50:42: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:50:43: 27000000 INFO @ Wed, 15 Apr 2020 23:50:44: 31000000 INFO @ Wed, 15 Apr 2020 23:50:50: 28000000 INFO @ Wed, 15 Apr 2020 23:50:52: 32000000 INFO @ Wed, 15 Apr 2020 23:50:58: 29000000 INFO @ Wed, 15 Apr 2020 23:50:59: 33000000 INFO @ Wed, 15 Apr 2020 23:51:02: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:51:06: 30000000 INFO @ Wed, 15 Apr 2020 23:51:07: 34000000 INFO @ Wed, 15 Apr 2020 23:51:13: 31000000 INFO @ Wed, 15 Apr 2020 23:51:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6619567/SRX6619567.05_peaks.xls INFO @ Wed, 15 Apr 2020 23:51:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6619567/SRX6619567.05_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:51:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6619567/SRX6619567.05_summits.bed INFO @ Wed, 15 Apr 2020 23:51:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (423 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 23:51:15: 35000000 INFO @ Wed, 15 Apr 2020 23:51:21: 32000000 INFO @ Wed, 15 Apr 2020 23:51:23: 36000000 INFO @ Wed, 15 Apr 2020 23:51:29: 33000000 INFO @ Wed, 15 Apr 2020 23:51:31: 37000000 INFO @ Wed, 15 Apr 2020 23:51:34: #1 tag size is determined as 150 bps INFO @ Wed, 15 Apr 2020 23:51:34: #1 tag size = 150 INFO @ Wed, 15 Apr 2020 23:51:34: #1 total tags in treatment: 11657390 INFO @ Wed, 15 Apr 2020 23:51:34: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:51:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 23:51:34: #1 tags after filtering in treatment: 9680731 INFO @ Wed, 15 Apr 2020 23:51:34: #1 Redundant rate of treatment: 0.17 INFO @ Wed, 15 Apr 2020 23:51:34: #1 finished! INFO @ Wed, 15 Apr 2020 23:51:34: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:51:34: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:51:34: #2 number of paired peaks: 374 WARNING @ Wed, 15 Apr 2020 23:51:34: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Wed, 15 Apr 2020 23:51:34: start model_add_line... INFO @ Wed, 15 Apr 2020 23:51:35: start X-correlation... INFO @ Wed, 15 Apr 2020 23:51:35: end of X-cor INFO @ Wed, 15 Apr 2020 23:51:35: #2 finished! INFO @ Wed, 15 Apr 2020 23:51:35: #2 predicted fragment length is 199 bps INFO @ Wed, 15 Apr 2020 23:51:35: #2 alternative fragment length(s) may be 199,217 bps INFO @ Wed, 15 Apr 2020 23:51:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6619567/SRX6619567.10_model.r WARNING @ Wed, 15 Apr 2020 23:51:35: #2 Since the d (199) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 23:51:35: #2 You may need to consider one of the other alternative d(s): 199,217 WARNING @ Wed, 15 Apr 2020 23:51:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 23:51:35: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:51:35: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:51:36: 34000000 INFO @ Wed, 15 Apr 2020 23:51:43: 35000000 INFO @ Wed, 15 Apr 2020 23:51:50: 36000000 INFO @ Wed, 15 Apr 2020 23:51:55: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:51:57: 37000000 INFO @ Wed, 15 Apr 2020 23:52:00: #1 tag size is determined as 150 bps INFO @ Wed, 15 Apr 2020 23:52:00: #1 tag size = 150 INFO @ Wed, 15 Apr 2020 23:52:00: #1 total tags in treatment: 11657390 INFO @ Wed, 15 Apr 2020 23:52:00: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 23:52:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 23:52:00: #1 tags after filtering in treatment: 9680731 INFO @ Wed, 15 Apr 2020 23:52:00: #1 Redundant rate of treatment: 0.17 INFO @ Wed, 15 Apr 2020 23:52:00: #1 finished! INFO @ Wed, 15 Apr 2020 23:52:00: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 23:52:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 23:52:00: #2 number of paired peaks: 374 WARNING @ Wed, 15 Apr 2020 23:52:00: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Wed, 15 Apr 2020 23:52:00: start model_add_line... INFO @ Wed, 15 Apr 2020 23:52:01: start X-correlation... INFO @ Wed, 15 Apr 2020 23:52:01: end of X-cor INFO @ Wed, 15 Apr 2020 23:52:01: #2 finished! INFO @ Wed, 15 Apr 2020 23:52:01: #2 predicted fragment length is 199 bps INFO @ Wed, 15 Apr 2020 23:52:01: #2 alternative fragment length(s) may be 199,217 bps INFO @ Wed, 15 Apr 2020 23:52:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6619567/SRX6619567.20_model.r WARNING @ Wed, 15 Apr 2020 23:52:01: #2 Since the d (199) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 23:52:01: #2 You may need to consider one of the other alternative d(s): 199,217 WARNING @ Wed, 15 Apr 2020 23:52:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 23:52:01: #3 Call peaks... INFO @ Wed, 15 Apr 2020 23:52:01: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 23:52:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6619567/SRX6619567.10_peaks.xls INFO @ Wed, 15 Apr 2020 23:52:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6619567/SRX6619567.10_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:52:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6619567/SRX6619567.10_summits.bed INFO @ Wed, 15 Apr 2020 23:52:06: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (300 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 23:52:21: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 23:52:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6619567/SRX6619567.20_peaks.xls INFO @ Wed, 15 Apr 2020 23:52:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6619567/SRX6619567.20_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 23:52:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6619567/SRX6619567.20_summits.bed INFO @ Wed, 15 Apr 2020 23:52:32: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (188 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。