Job ID = 6497388 SRX = SRX4085368 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T21:22:59 prefetch.2.10.7: 1) Downloading 'SRR7167397'... 2020-06-25T21:22:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T21:28:45 prefetch.2.10.7: HTTPS download succeed 2020-06-25T21:28:45 prefetch.2.10.7: 1) 'SRR7167397' was downloaded successfully Read 23665306 spots for SRR7167397/SRR7167397.sra Written 23665306 spots for SRR7167397/SRR7167397.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: 00:19:02 23665306 reads; of these: 23665306 (100.00%) were paired; of these: 6693475 (28.28%) aligned concordantly 0 times 14681121 (62.04%) aligned concordantly exactly 1 time 2290710 (9.68%) aligned concordantly >1 times ---- 6693475 pairs aligned concordantly 0 times; of these: 300804 (4.49%) aligned discordantly 1 time ---- 6392671 pairs aligned 0 times concordantly or discordantly; of these: 12785342 mates make up the pairs; of these: 10308608 (80.63%) aligned 0 times 2164535 (16.93%) aligned exactly 1 time 312199 (2.44%) aligned >1 times 78.22% overall alignment rate Time searching: 00:19:02 Overall time: 00:19:02 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 16 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] 1313760 / 17157943 = 0.0766 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 @ Fri, 26 Jun 2020 07:03:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4085368/SRX4085368.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4085368/SRX4085368.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4085368/SRX4085368.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4085368/SRX4085368.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 @ Fri, 26 Jun 2020 07:03:15: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:03:15: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:03:24: 1000000 INFO @ Fri, 26 Jun 2020 07:03:34: 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 @ Fri, 26 Jun 2020 07:03:44: 3000000 INFO @ Fri, 26 Jun 2020 07:03:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4085368/SRX4085368.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4085368/SRX4085368.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4085368/SRX4085368.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4085368/SRX4085368.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 @ Fri, 26 Jun 2020 07:03:45: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:03:45: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:03:53: 4000000 INFO @ Fri, 26 Jun 2020 07:03:55: 1000000 INFO @ Fri, 26 Jun 2020 07:04:03: 5000000 INFO @ Fri, 26 Jun 2020 07:04:05: 2000000 INFO @ Fri, 26 Jun 2020 07:04:13: 6000000 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 @ Fri, 26 Jun 2020 07:04:15: 3000000 INFO @ Fri, 26 Jun 2020 07:04:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4085368/SRX4085368.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4085368/SRX4085368.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4085368/SRX4085368.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4085368/SRX4085368.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 @ Fri, 26 Jun 2020 07:04:15: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:04:15: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:04:23: 7000000 INFO @ Fri, 26 Jun 2020 07:04:24: 1000000 INFO @ Fri, 26 Jun 2020 07:04:25: 4000000 INFO @ Fri, 26 Jun 2020 07:04:33: 2000000 INFO @ Fri, 26 Jun 2020 07:04:33: 8000000 INFO @ Fri, 26 Jun 2020 07:04:35: 5000000 INFO @ Fri, 26 Jun 2020 07:04:41: 3000000 INFO @ Fri, 26 Jun 2020 07:04:43: 9000000 INFO @ Fri, 26 Jun 2020 07:04:45: 6000000 INFO @ Fri, 26 Jun 2020 07:04:50: 4000000 INFO @ Fri, 26 Jun 2020 07:04:53: 10000000 INFO @ Fri, 26 Jun 2020 07:04:55: 7000000 INFO @ Fri, 26 Jun 2020 07:04:58: 5000000 INFO @ Fri, 26 Jun 2020 07:05:03: 11000000 INFO @ Fri, 26 Jun 2020 07:05:05: 8000000 INFO @ Fri, 26 Jun 2020 07:05:07: 6000000 INFO @ Fri, 26 Jun 2020 07:05:13: 12000000 INFO @ Fri, 26 Jun 2020 07:05:15: 9000000 INFO @ Fri, 26 Jun 2020 07:05:16: 7000000 INFO @ Fri, 26 Jun 2020 07:05:23: 13000000 INFO @ Fri, 26 Jun 2020 07:05:24: 8000000 INFO @ Fri, 26 Jun 2020 07:05:25: 10000000 INFO @ Fri, 26 Jun 2020 07:05:33: 9000000 INFO @ Fri, 26 Jun 2020 07:05:34: 14000000 INFO @ Fri, 26 Jun 2020 07:05:36: 11000000 INFO @ Fri, 26 Jun 2020 07:05:41: 10000000 INFO @ Fri, 26 Jun 2020 07:05:44: 15000000 INFO @ Fri, 26 Jun 2020 07:05:46: 12000000 INFO @ Fri, 26 Jun 2020 07:05:50: 11000000 INFO @ Fri, 26 Jun 2020 07:05:54: 16000000 INFO @ Fri, 26 Jun 2020 07:05:56: 13000000 INFO @ Fri, 26 Jun 2020 07:05:59: 12000000 INFO @ Fri, 26 Jun 2020 07:06:04: 17000000 INFO @ Fri, 26 Jun 2020 07:06:06: 14000000 INFO @ Fri, 26 Jun 2020 07:06:07: 13000000 INFO @ Fri, 26 Jun 2020 07:06:14: 18000000 INFO @ Fri, 26 Jun 2020 07:06:16: 14000000 INFO @ Fri, 26 Jun 2020 07:06:16: 15000000 INFO @ Fri, 26 Jun 2020 07:06:24: 19000000 INFO @ Fri, 26 Jun 2020 07:06:24: 15000000 INFO @ Fri, 26 Jun 2020 07:06:26: 16000000 INFO @ Fri, 26 Jun 2020 07:06:34: 16000000 INFO @ Fri, 26 Jun 2020 07:06:34: 20000000 INFO @ Fri, 26 Jun 2020 07:06:36: 17000000 INFO @ Fri, 26 Jun 2020 07:06:42: 17000000 INFO @ Fri, 26 Jun 2020 07:06:44: 21000000 INFO @ Fri, 26 Jun 2020 07:06:46: 18000000 INFO @ Fri, 26 Jun 2020 07:06:51: 18000000 INFO @ Fri, 26 Jun 2020 07:06:54: 22000000 INFO @ Fri, 26 Jun 2020 07:06:56: 19000000 INFO @ Fri, 26 Jun 2020 07:07:00: 19000000 INFO @ Fri, 26 Jun 2020 07:07:04: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:07:06: 20000000 INFO @ Fri, 26 Jun 2020 07:07:08: 20000000 INFO @ Fri, 26 Jun 2020 07:07:14: 24000000 INFO @ Fri, 26 Jun 2020 07:07:15: 21000000 INFO @ Fri, 26 Jun 2020 07:07:16: 21000000 INFO @ Fri, 26 Jun 2020 07:07:23: 25000000 INFO @ Fri, 26 Jun 2020 07:07:24: 22000000 INFO @ Fri, 26 Jun 2020 07:07:24: 22000000 INFO @ Fri, 26 Jun 2020 07:07:32: 23000000 INFO @ Fri, 26 Jun 2020 07:07:33: 26000000 INFO @ Fri, 26 Jun 2020 07:07:33: 23000000 INFO @ Fri, 26 Jun 2020 07:07:40: 24000000 INFO @ Fri, 26 Jun 2020 07:07:42: 27000000 INFO @ Fri, 26 Jun 2020 07:07:42: 24000000 INFO @ Fri, 26 Jun 2020 07:07:48: 25000000 INFO @ Fri, 26 Jun 2020 07:07:51: 28000000 INFO @ Fri, 26 Jun 2020 07:07:51: 25000000 INFO @ Fri, 26 Jun 2020 07:07:56: 26000000 INFO @ Fri, 26 Jun 2020 07:08:00: 26000000 INFO @ Fri, 26 Jun 2020 07:08:00: 29000000 INFO @ Fri, 26 Jun 2020 07:08:03: 27000000 INFO @ Fri, 26 Jun 2020 07:08:09: 27000000 INFO @ Fri, 26 Jun 2020 07:08:09: 30000000 INFO @ Fri, 26 Jun 2020 07:08:11: 28000000 INFO @ Fri, 26 Jun 2020 07:08:18: 28000000 INFO @ Fri, 26 Jun 2020 07:08:18: 31000000 INFO @ Fri, 26 Jun 2020 07:08:19: 29000000 INFO @ Fri, 26 Jun 2020 07:08:26: 30000000 INFO @ Fri, 26 Jun 2020 07:08:26: 29000000 INFO @ Fri, 26 Jun 2020 07:08:27: 32000000 INFO @ Fri, 26 Jun 2020 07:08:34: 31000000 INFO @ Fri, 26 Jun 2020 07:08:35: 30000000 INFO @ Fri, 26 Jun 2020 07:08:35: 33000000 INFO @ Fri, 26 Jun 2020 07:08:41: 32000000 INFO @ Fri, 26 Jun 2020 07:08:43: 34000000 INFO @ Fri, 26 Jun 2020 07:08:43: 31000000 INFO @ Fri, 26 Jun 2020 07:08:46: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 07:08:46: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 07:08:46: #1 total tags in treatment: 15672591 INFO @ Fri, 26 Jun 2020 07:08:46: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:08:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:08:46: #1 tags after filtering in treatment: 13532147 INFO @ Fri, 26 Jun 2020 07:08:46: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 26 Jun 2020 07:08:46: #1 finished! INFO @ Fri, 26 Jun 2020 07:08:46: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:08:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:08:47: #2 number of paired peaks: 270 WARNING @ Fri, 26 Jun 2020 07:08:47: Fewer paired peaks (270) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 270 pairs to build model! INFO @ Fri, 26 Jun 2020 07:08:47: start model_add_line... INFO @ Fri, 26 Jun 2020 07:08:47: start X-correlation... INFO @ Fri, 26 Jun 2020 07:08:47: end of X-cor INFO @ Fri, 26 Jun 2020 07:08:47: #2 finished! INFO @ Fri, 26 Jun 2020 07:08:47: #2 predicted fragment length is 97 bps INFO @ Fri, 26 Jun 2020 07:08:47: #2 alternative fragment length(s) may be 4,97 bps INFO @ Fri, 26 Jun 2020 07:08:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4085368/SRX4085368.05_model.r INFO @ Fri, 26 Jun 2020 07:08:49: 33000000 INFO @ Fri, 26 Jun 2020 07:08:50: 32000000 INFO @ Fri, 26 Jun 2020 07:08:56: 34000000 INFO @ Fri, 26 Jun 2020 07:08:58: 33000000 INFO @ Fri, 26 Jun 2020 07:08:59: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 07:08:59: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 07:08:59: #1 total tags in treatment: 15672591 INFO @ Fri, 26 Jun 2020 07:08:59: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:08:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:08:59: #1 tags after filtering in treatment: 13532147 INFO @ Fri, 26 Jun 2020 07:08:59: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 26 Jun 2020 07:08:59: #1 finished! INFO @ Fri, 26 Jun 2020 07:08:59: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:08:59: #2 looking for paired plus/minus strand peaks... WARNING @ Fri, 26 Jun 2020 07:08:59: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:08:59: #2 You may need to consider one of the other alternative d(s): 4,97 WARNING @ Fri, 26 Jun 2020 07:08:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:08:59: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:08:59: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:09:00: #2 number of paired peaks: 270 WARNING @ Fri, 26 Jun 2020 07:09:00: Fewer paired peaks (270) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 270 pairs to build model! INFO @ Fri, 26 Jun 2020 07:09:00: start model_add_line... INFO @ Fri, 26 Jun 2020 07:09:00: start X-correlation... INFO @ Fri, 26 Jun 2020 07:09:00: end of X-cor INFO @ Fri, 26 Jun 2020 07:09:00: #2 finished! INFO @ Fri, 26 Jun 2020 07:09:00: #2 predicted fragment length is 97 bps INFO @ Fri, 26 Jun 2020 07:09:00: #2 alternative fragment length(s) may be 4,97 bps INFO @ Fri, 26 Jun 2020 07:09:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4085368/SRX4085368.20_model.r WARNING @ Fri, 26 Jun 2020 07:09:00: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:09:00: #2 You may need to consider one of the other alternative d(s): 4,97 WARNING @ Fri, 26 Jun 2020 07:09:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:09:00: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:09:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:09:05: 34000000 INFO @ Fri, 26 Jun 2020 07:09:07: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 07:09:07: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 07:09:07: #1 total tags in treatment: 15672591 INFO @ Fri, 26 Jun 2020 07:09:07: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:09:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:09:08: #1 tags after filtering in treatment: 13532147 INFO @ Fri, 26 Jun 2020 07:09:08: #1 Redundant rate of treatment: 0.14 INFO @ Fri, 26 Jun 2020 07:09:08: #1 finished! INFO @ Fri, 26 Jun 2020 07:09:08: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:09:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:09:09: #2 number of paired peaks: 270 WARNING @ Fri, 26 Jun 2020 07:09:09: Fewer paired peaks (270) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 270 pairs to build model! INFO @ Fri, 26 Jun 2020 07:09:09: start model_add_line... INFO @ Fri, 26 Jun 2020 07:09:09: start X-correlation... INFO @ Fri, 26 Jun 2020 07:09:09: end of X-cor INFO @ Fri, 26 Jun 2020 07:09:09: #2 finished! INFO @ Fri, 26 Jun 2020 07:09:09: #2 predicted fragment length is 97 bps INFO @ Fri, 26 Jun 2020 07:09:09: #2 alternative fragment length(s) may be 4,97 bps INFO @ Fri, 26 Jun 2020 07:09:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4085368/SRX4085368.10_model.r WARNING @ Fri, 26 Jun 2020 07:09:09: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:09:09: #2 You may need to consider one of the other alternative d(s): 4,97 WARNING @ Fri, 26 Jun 2020 07:09:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:09:09: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:09:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:09:24: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:09:24: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:09:33: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:09:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4085368/SRX4085368.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:09:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4085368/SRX4085368.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:09:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4085368/SRX4085368.05_summits.bed INFO @ Fri, 26 Jun 2020 07:09:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3756 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:09:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4085368/SRX4085368.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:09:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4085368/SRX4085368.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:09:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4085368/SRX4085368.20_summits.bed INFO @ Fri, 26 Jun 2020 07:09:37: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1129 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:09:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4085368/SRX4085368.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:09:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4085368/SRX4085368.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:09:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4085368/SRX4085368.10_summits.bed INFO @ Fri, 26 Jun 2020 07:09:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2294 records, 4 fields): 4 millis CompletedMACS2peakCalling