Job ID = 12264764 SRX = SRX3029129 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 65633087 spots for SRR5860429/SRR5860429.sra Written 65633087 spots for SRR5860429/SRR5860429.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265612 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:57:31 65633087 reads; of these: 65633087 (100.00%) were paired; of these: 35979671 (54.82%) aligned concordantly 0 times 24095080 (36.71%) aligned concordantly exactly 1 time 5558336 (8.47%) aligned concordantly >1 times ---- 35979671 pairs aligned concordantly 0 times; of these: 5315950 (14.77%) aligned discordantly 1 time ---- 30663721 pairs aligned 0 times concordantly or discordantly; of these: 61327442 mates make up the pairs; of these: 58356051 (95.15%) aligned 0 times 1167410 (1.90%) aligned exactly 1 time 1803981 (2.94%) aligned >1 times 55.54% overall alignment rate Time searching: 00:57:31 Overall time: 00:57:31 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 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] 17388585 / 34545070 = 0.5034 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:48:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3029129/SRX3029129.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3029129/SRX3029129.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3029129/SRX3029129.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3029129/SRX3029129.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 @ Sat, 03 Apr 2021 07:48:13: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:48:13: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:48:20: 1000000 INFO @ Sat, 03 Apr 2021 07:48:25: 2000000 INFO @ Sat, 03 Apr 2021 07:48:31: 3000000 INFO @ Sat, 03 Apr 2021 07:48:37: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:48:42: 5000000 INFO @ Sat, 03 Apr 2021 07:48:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3029129/SRX3029129.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3029129/SRX3029129.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3029129/SRX3029129.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3029129/SRX3029129.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 @ Sat, 03 Apr 2021 07:48:43: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:48:43: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:48:48: 6000000 INFO @ Sat, 03 Apr 2021 07:48:49: 1000000 INFO @ Sat, 03 Apr 2021 07:48:55: 7000000 INFO @ Sat, 03 Apr 2021 07:48:56: 2000000 INFO @ Sat, 03 Apr 2021 07:49:01: 8000000 INFO @ Sat, 03 Apr 2021 07:49:02: 3000000 INFO @ Sat, 03 Apr 2021 07:49:07: 9000000 INFO @ Sat, 03 Apr 2021 07:49:08: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:49:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3029129/SRX3029129.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3029129/SRX3029129.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3029129/SRX3029129.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3029129/SRX3029129.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 @ Sat, 03 Apr 2021 07:49:13: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:49:13: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:49:13: 10000000 INFO @ Sat, 03 Apr 2021 07:49:14: 5000000 INFO @ Sat, 03 Apr 2021 07:49:20: 1000000 INFO @ Sat, 03 Apr 2021 07:49:20: 11000000 INFO @ Sat, 03 Apr 2021 07:49:21: 6000000 INFO @ Sat, 03 Apr 2021 07:49:27: 2000000 INFO @ Sat, 03 Apr 2021 07:49:27: 12000000 INFO @ Sat, 03 Apr 2021 07:49:28: 7000000 INFO @ Sat, 03 Apr 2021 07:49:34: 3000000 INFO @ Sat, 03 Apr 2021 07:49:34: 13000000 INFO @ Sat, 03 Apr 2021 07:49:35: 8000000 INFO @ Sat, 03 Apr 2021 07:49:41: 4000000 INFO @ Sat, 03 Apr 2021 07:49:41: 14000000 INFO @ Sat, 03 Apr 2021 07:49:42: 9000000 INFO @ Sat, 03 Apr 2021 07:49:48: 5000000 INFO @ Sat, 03 Apr 2021 07:49:48: 15000000 INFO @ Sat, 03 Apr 2021 07:49:49: 10000000 INFO @ Sat, 03 Apr 2021 07:49:55: 6000000 INFO @ Sat, 03 Apr 2021 07:49:56: 16000000 INFO @ Sat, 03 Apr 2021 07:49:56: 11000000 INFO @ Sat, 03 Apr 2021 07:50:02: 7000000 INFO @ Sat, 03 Apr 2021 07:50:03: 17000000 INFO @ Sat, 03 Apr 2021 07:50:03: 12000000 INFO @ Sat, 03 Apr 2021 07:50:09: 8000000 INFO @ Sat, 03 Apr 2021 07:50:10: 18000000 INFO @ Sat, 03 Apr 2021 07:50:10: 13000000 INFO @ Sat, 03 Apr 2021 07:50:16: 9000000 INFO @ Sat, 03 Apr 2021 07:50:17: 19000000 INFO @ Sat, 03 Apr 2021 07:50:17: 14000000 INFO @ Sat, 03 Apr 2021 07:50:22: 10000000 INFO @ Sat, 03 Apr 2021 07:50:24: 20000000 INFO @ Sat, 03 Apr 2021 07:50:24: 15000000 INFO @ Sat, 03 Apr 2021 07:50:29: 11000000 INFO @ Sat, 03 Apr 2021 07:50:31: 21000000 INFO @ Sat, 03 Apr 2021 07:50:31: 16000000 INFO @ Sat, 03 Apr 2021 07:50:37: 12000000 INFO @ Sat, 03 Apr 2021 07:50:38: 22000000 INFO @ Sat, 03 Apr 2021 07:50:38: 17000000 INFO @ Sat, 03 Apr 2021 07:50:44: 13000000 INFO @ Sat, 03 Apr 2021 07:50:45: 23000000 INFO @ Sat, 03 Apr 2021 07:50:45: 18000000 INFO @ Sat, 03 Apr 2021 07:50:50: 14000000 INFO @ Sat, 03 Apr 2021 07:50:52: 24000000 INFO @ Sat, 03 Apr 2021 07:50:52: 19000000 INFO @ Sat, 03 Apr 2021 07:50:58: 15000000 INFO @ Sat, 03 Apr 2021 07:50:59: 25000000 INFO @ Sat, 03 Apr 2021 07:51:00: 20000000 INFO @ Sat, 03 Apr 2021 07:51:06: 16000000 INFO @ Sat, 03 Apr 2021 07:51:07: 26000000 INFO @ Sat, 03 Apr 2021 07:51:07: 21000000 INFO @ Sat, 03 Apr 2021 07:51:13: 17000000 INFO @ Sat, 03 Apr 2021 07:51:14: 27000000 INFO @ Sat, 03 Apr 2021 07:51:15: 22000000 INFO @ Sat, 03 Apr 2021 07:51:21: 18000000 INFO @ Sat, 03 Apr 2021 07:51:21: 28000000 INFO @ Sat, 03 Apr 2021 07:51:22: 23000000 INFO @ Sat, 03 Apr 2021 07:51:28: 19000000 INFO @ Sat, 03 Apr 2021 07:51:29: 29000000 INFO @ Sat, 03 Apr 2021 07:51:30: 24000000 INFO @ Sat, 03 Apr 2021 07:51:36: 30000000 INFO @ Sat, 03 Apr 2021 07:51:36: 20000000 INFO @ Sat, 03 Apr 2021 07:51:37: 25000000 INFO @ Sat, 03 Apr 2021 07:51:44: 31000000 INFO @ Sat, 03 Apr 2021 07:51:44: 21000000 INFO @ Sat, 03 Apr 2021 07:51:45: 26000000 INFO @ Sat, 03 Apr 2021 07:51:51: 32000000 INFO @ Sat, 03 Apr 2021 07:51:52: 27000000 INFO @ Sat, 03 Apr 2021 07:51:53: 22000000 INFO @ Sat, 03 Apr 2021 07:51:58: 33000000 INFO @ Sat, 03 Apr 2021 07:51:59: 28000000 INFO @ Sat, 03 Apr 2021 07:52:00: 23000000 INFO @ Sat, 03 Apr 2021 07:52:05: 34000000 INFO @ Sat, 03 Apr 2021 07:52:06: 29000000 INFO @ Sat, 03 Apr 2021 07:52:08: 24000000 INFO @ Sat, 03 Apr 2021 07:52:13: 35000000 INFO @ Sat, 03 Apr 2021 07:52:14: 30000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:52:15: 25000000 INFO @ Sat, 03 Apr 2021 07:52:21: 31000000 INFO @ Sat, 03 Apr 2021 07:52:21: 36000000 INFO @ Sat, 03 Apr 2021 07:52:22: 26000000 INFO @ Sat, 03 Apr 2021 07:52:28: 32000000 INFO @ Sat, 03 Apr 2021 07:52:29: 37000000 INFO @ Sat, 03 Apr 2021 07:52:30: 27000000 INFO @ Sat, 03 Apr 2021 07:52:36: 33000000 INFO @ Sat, 03 Apr 2021 07:52:36: 38000000 INFO @ Sat, 03 Apr 2021 07:52:37: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 07:52:37: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 07:52:37: #1 total tags in treatment: 14908252 INFO @ Sat, 03 Apr 2021 07:52:37: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:52:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:52:37: 28000000 INFO @ Sat, 03 Apr 2021 07:52:37: #1 tags after filtering in treatment: 9923305 INFO @ Sat, 03 Apr 2021 07:52:37: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 03 Apr 2021 07:52:37: #1 finished! INFO @ Sat, 03 Apr 2021 07:52:37: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:52:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:52:38: #2 number of paired peaks: 756 WARNING @ Sat, 03 Apr 2021 07:52:38: Fewer paired peaks (756) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 756 pairs to build model! INFO @ Sat, 03 Apr 2021 07:52:38: start model_add_line... INFO @ Sat, 03 Apr 2021 07:52:38: start X-correlation... INFO @ Sat, 03 Apr 2021 07:52:38: end of X-cor INFO @ Sat, 03 Apr 2021 07:52:38: #2 finished! INFO @ Sat, 03 Apr 2021 07:52:38: #2 predicted fragment length is 123 bps INFO @ Sat, 03 Apr 2021 07:52:38: #2 alternative fragment length(s) may be 123 bps INFO @ Sat, 03 Apr 2021 07:52:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3029129/SRX3029129.05_model.r WARNING @ Sat, 03 Apr 2021 07:52:38: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:52:38: #2 You may need to consider one of the other alternative d(s): 123 WARNING @ Sat, 03 Apr 2021 07:52:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:52:38: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:52:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:52:43: 34000000 INFO @ Sat, 03 Apr 2021 07:52:44: 29000000 INFO @ Sat, 03 Apr 2021 07:52:50: 35000000 INFO @ Sat, 03 Apr 2021 07:52:51: 30000000 INFO @ Sat, 03 Apr 2021 07:52:57: 36000000 INFO @ Sat, 03 Apr 2021 07:52:58: 31000000 INFO @ Sat, 03 Apr 2021 07:53:00: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:53:04: 37000000 INFO @ Sat, 03 Apr 2021 07:53:05: 32000000 INFO @ Sat, 03 Apr 2021 07:53:12: 38000000 INFO @ Sat, 03 Apr 2021 07:53:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3029129/SRX3029129.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:53:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3029129/SRX3029129.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:53:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3029129/SRX3029129.05_summits.bed INFO @ Sat, 03 Apr 2021 07:53:12: Done! INFO @ Sat, 03 Apr 2021 07:53:12: 33000000 pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (9301 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:53:13: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 07:53:13: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 07:53:13: #1 total tags in treatment: 14908252 INFO @ Sat, 03 Apr 2021 07:53:13: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:53:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:53:13: #1 tags after filtering in treatment: 9923305 INFO @ Sat, 03 Apr 2021 07:53:13: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 03 Apr 2021 07:53:13: #1 finished! INFO @ Sat, 03 Apr 2021 07:53:13: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:53:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:53:14: #2 number of paired peaks: 756 WARNING @ Sat, 03 Apr 2021 07:53:14: Fewer paired peaks (756) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 756 pairs to build model! INFO @ Sat, 03 Apr 2021 07:53:14: start model_add_line... INFO @ Sat, 03 Apr 2021 07:53:14: start X-correlation... INFO @ Sat, 03 Apr 2021 07:53:14: end of X-cor INFO @ Sat, 03 Apr 2021 07:53:14: #2 finished! INFO @ Sat, 03 Apr 2021 07:53:14: #2 predicted fragment length is 123 bps INFO @ Sat, 03 Apr 2021 07:53:14: #2 alternative fragment length(s) may be 123 bps INFO @ Sat, 03 Apr 2021 07:53:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3029129/SRX3029129.10_model.r WARNING @ Sat, 03 Apr 2021 07:53:14: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:53:14: #2 You may need to consider one of the other alternative d(s): 123 WARNING @ Sat, 03 Apr 2021 07:53:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:53:14: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:53:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:53:19: 34000000 INFO @ Sat, 03 Apr 2021 07:53:26: 35000000 INFO @ Sat, 03 Apr 2021 07:53:33: 36000000 INFO @ Sat, 03 Apr 2021 07:53:35: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:53:40: 37000000 INFO @ Sat, 03 Apr 2021 07:53:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3029129/SRX3029129.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:53:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3029129/SRX3029129.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:53:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3029129/SRX3029129.10_summits.bed INFO @ Sat, 03 Apr 2021 07:53:47: Done! INFO @ Sat, 03 Apr 2021 07:53:47: 38000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5067 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:53:48: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 07:53:48: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 07:53:48: #1 total tags in treatment: 14908252 INFO @ Sat, 03 Apr 2021 07:53:48: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:53:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:53:48: #1 tags after filtering in treatment: 9923305 INFO @ Sat, 03 Apr 2021 07:53:48: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 03 Apr 2021 07:53:48: #1 finished! INFO @ Sat, 03 Apr 2021 07:53:48: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:53:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:53:49: #2 number of paired peaks: 756 WARNING @ Sat, 03 Apr 2021 07:53:49: Fewer paired peaks (756) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 756 pairs to build model! INFO @ Sat, 03 Apr 2021 07:53:49: start model_add_line... INFO @ Sat, 03 Apr 2021 07:53:49: start X-correlation... INFO @ Sat, 03 Apr 2021 07:53:49: end of X-cor INFO @ Sat, 03 Apr 2021 07:53:49: #2 finished! INFO @ Sat, 03 Apr 2021 07:53:49: #2 predicted fragment length is 123 bps INFO @ Sat, 03 Apr 2021 07:53:49: #2 alternative fragment length(s) may be 123 bps INFO @ Sat, 03 Apr 2021 07:53:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3029129/SRX3029129.20_model.r WARNING @ Sat, 03 Apr 2021 07:53:49: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:53:49: #2 You may need to consider one of the other alternative d(s): 123 WARNING @ Sat, 03 Apr 2021 07:53:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:53:49: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:53:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:54:10: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:54:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3029129/SRX3029129.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:54:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3029129/SRX3029129.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:54:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3029129/SRX3029129.20_summits.bed INFO @ Sat, 03 Apr 2021 07:54:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2396 records, 4 fields): 4 millis CompletedMACS2peakCalling