Job ID = 6366578 SRX = SRX2011718 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T22:59:08 prefetch.2.10.7: 1) Downloading 'SRR4017960'... 2020-06-15T22:59:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:01:44 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:01:44 prefetch.2.10.7: 1) 'SRR4017960' was downloaded successfully Read 9344677 spots for SRR4017960/SRR4017960.sra Written 9344677 spots for SRR4017960/SRR4017960.sra 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: 00:17:09 9344677 reads; of these: 9344677 (100.00%) were paired; of these: 806087 (8.63%) aligned concordantly 0 times 7394927 (79.14%) aligned concordantly exactly 1 time 1143663 (12.24%) aligned concordantly >1 times ---- 806087 pairs aligned concordantly 0 times; of these: 580059 (71.96%) aligned discordantly 1 time ---- 226028 pairs aligned 0 times concordantly or discordantly; of these: 452056 mates make up the pairs; of these: 165871 (36.69%) aligned 0 times 130050 (28.77%) aligned exactly 1 time 156135 (34.54%) aligned >1 times 99.11% overall alignment rate Time searching: 00:17:10 Overall time: 00:17:10 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 8 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] 396010 / 9009640 = 0.0440 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 08:30:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2011718/SRX2011718.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2011718/SRX2011718.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2011718/SRX2011718.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2011718/SRX2011718.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 08:30:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:30:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:30:53: 1000000 INFO @ Tue, 16 Jun 2020 08:30:59: 2000000 INFO @ Tue, 16 Jun 2020 08:31:06: 3000000 INFO @ Tue, 16 Jun 2020 08:31:13: 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 08:31:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2011718/SRX2011718.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2011718/SRX2011718.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2011718/SRX2011718.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2011718/SRX2011718.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 08:31:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:31:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:20: 5000000 INFO @ Tue, 16 Jun 2020 08:31:23: 1000000 INFO @ Tue, 16 Jun 2020 08:31:27: 6000000 INFO @ Tue, 16 Jun 2020 08:31:31: 2000000 INFO @ Tue, 16 Jun 2020 08:31:34: 7000000 INFO @ Tue, 16 Jun 2020 08:31:38: 3000000 INFO @ Tue, 16 Jun 2020 08:31:41: 8000000 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 08:31:45: 4000000 INFO @ Tue, 16 Jun 2020 08:31:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2011718/SRX2011718.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2011718/SRX2011718.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2011718/SRX2011718.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2011718/SRX2011718.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 08:31:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:31:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:48: 9000000 INFO @ Tue, 16 Jun 2020 08:31:51: 5000000 INFO @ Tue, 16 Jun 2020 08:31:53: 1000000 INFO @ Tue, 16 Jun 2020 08:31:54: 10000000 INFO @ Tue, 16 Jun 2020 08:31:58: 6000000 INFO @ Tue, 16 Jun 2020 08:32:00: 2000000 INFO @ Tue, 16 Jun 2020 08:32:02: 11000000 INFO @ Tue, 16 Jun 2020 08:32:06: 7000000 INFO @ Tue, 16 Jun 2020 08:32:06: 3000000 INFO @ Tue, 16 Jun 2020 08:32:09: 12000000 INFO @ Tue, 16 Jun 2020 08:32:13: 8000000 INFO @ Tue, 16 Jun 2020 08:32:13: 4000000 INFO @ Tue, 16 Jun 2020 08:32:16: 13000000 INFO @ Tue, 16 Jun 2020 08:32:19: 5000000 INFO @ Tue, 16 Jun 2020 08:32:20: 9000000 INFO @ Tue, 16 Jun 2020 08:32:23: 14000000 INFO @ Tue, 16 Jun 2020 08:32:26: 6000000 INFO @ Tue, 16 Jun 2020 08:32:28: 10000000 INFO @ Tue, 16 Jun 2020 08:32:31: 15000000 INFO @ Tue, 16 Jun 2020 08:32:32: 7000000 INFO @ Tue, 16 Jun 2020 08:32:35: 11000000 INFO @ Tue, 16 Jun 2020 08:32:38: 8000000 INFO @ Tue, 16 Jun 2020 08:32:39: 16000000 INFO @ Tue, 16 Jun 2020 08:32:43: 12000000 INFO @ Tue, 16 Jun 2020 08:32:45: 9000000 INFO @ Tue, 16 Jun 2020 08:32:46: 17000000 INFO @ Tue, 16 Jun 2020 08:32:51: 13000000 INFO @ Tue, 16 Jun 2020 08:32:51: 10000000 INFO @ Tue, 16 Jun 2020 08:32:52: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:32:52: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:32:52: #1 total tags in treatment: 8152824 INFO @ Tue, 16 Jun 2020 08:32:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:32:52: #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 08:32:52: #1 tags after filtering in treatment: 7648751 INFO @ Tue, 16 Jun 2020 08:32:52: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 16 Jun 2020 08:32:52: #1 finished! INFO @ Tue, 16 Jun 2020 08:32:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:32:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:32:52: #2 number of paired peaks: 347 WARNING @ Tue, 16 Jun 2020 08:32:52: Fewer paired peaks (347) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 347 pairs to build model! INFO @ Tue, 16 Jun 2020 08:32:52: start model_add_line... INFO @ Tue, 16 Jun 2020 08:32:53: start X-correlation... INFO @ Tue, 16 Jun 2020 08:32:53: end of X-cor INFO @ Tue, 16 Jun 2020 08:32:53: #2 finished! INFO @ Tue, 16 Jun 2020 08:32:53: #2 predicted fragment length is 173 bps INFO @ Tue, 16 Jun 2020 08:32:53: #2 alternative fragment length(s) may be 173 bps INFO @ Tue, 16 Jun 2020 08:32:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2011718/SRX2011718.05_model.r WARNING @ Tue, 16 Jun 2020 08:32:53: #2 Since the d (173) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:32:53: #2 You may need to consider one of the other alternative d(s): 173 WARNING @ Tue, 16 Jun 2020 08:32:53: #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 08:32:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:32:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:32:57: 14000000 INFO @ Tue, 16 Jun 2020 08:32:58: 11000000 INFO @ Tue, 16 Jun 2020 08:33:04: 15000000 INFO @ Tue, 16 Jun 2020 08:33:04: 12000000 INFO @ Tue, 16 Jun 2020 08:33:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:33:10: 16000000 INFO @ Tue, 16 Jun 2020 08:33:10: 13000000 INFO @ Tue, 16 Jun 2020 08:33:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2011718/SRX2011718.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:33:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2011718/SRX2011718.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:33:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2011718/SRX2011718.05_summits.bed INFO @ Tue, 16 Jun 2020 08:33:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (349 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:33:16: 17000000 INFO @ Tue, 16 Jun 2020 08:33:17: 14000000 INFO @ Tue, 16 Jun 2020 08:33:21: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:33:21: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:33:21: #1 total tags in treatment: 8152824 INFO @ Tue, 16 Jun 2020 08:33:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:33:21: #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 08:33:21: #1 tags after filtering in treatment: 7648751 INFO @ Tue, 16 Jun 2020 08:33:21: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 16 Jun 2020 08:33:21: #1 finished! INFO @ Tue, 16 Jun 2020 08:33:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:33:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:33:21: #2 number of paired peaks: 347 WARNING @ Tue, 16 Jun 2020 08:33:21: Fewer paired peaks (347) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 347 pairs to build model! INFO @ Tue, 16 Jun 2020 08:33:21: start model_add_line... INFO @ Tue, 16 Jun 2020 08:33:21: start X-correlation... INFO @ Tue, 16 Jun 2020 08:33:21: end of X-cor INFO @ Tue, 16 Jun 2020 08:33:21: #2 finished! INFO @ Tue, 16 Jun 2020 08:33:21: #2 predicted fragment length is 173 bps INFO @ Tue, 16 Jun 2020 08:33:21: #2 alternative fragment length(s) may be 173 bps INFO @ Tue, 16 Jun 2020 08:33:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2011718/SRX2011718.10_model.r WARNING @ Tue, 16 Jun 2020 08:33:21: #2 Since the d (173) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:33:21: #2 You may need to consider one of the other alternative d(s): 173 WARNING @ Tue, 16 Jun 2020 08:33:21: #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 08:33:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:33:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:33:23: 15000000 INFO @ Tue, 16 Jun 2020 08:33:29: 16000000 INFO @ Tue, 16 Jun 2020 08:33:36: 17000000 INFO @ Tue, 16 Jun 2020 08:33:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:33:40: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:33:40: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:33:40: #1 total tags in treatment: 8152824 INFO @ Tue, 16 Jun 2020 08:33:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:33:40: #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 08:33:40: #1 tags after filtering in treatment: 7648751 INFO @ Tue, 16 Jun 2020 08:33:40: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 16 Jun 2020 08:33:40: #1 finished! INFO @ Tue, 16 Jun 2020 08:33:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:33:40: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:33:41: #2 number of paired peaks: 347 WARNING @ Tue, 16 Jun 2020 08:33:41: Fewer paired peaks (347) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 347 pairs to build model! INFO @ Tue, 16 Jun 2020 08:33:41: start model_add_line... INFO @ Tue, 16 Jun 2020 08:33:41: start X-correlation... INFO @ Tue, 16 Jun 2020 08:33:41: end of X-cor INFO @ Tue, 16 Jun 2020 08:33:41: #2 finished! INFO @ Tue, 16 Jun 2020 08:33:41: #2 predicted fragment length is 173 bps INFO @ Tue, 16 Jun 2020 08:33:41: #2 alternative fragment length(s) may be 173 bps INFO @ Tue, 16 Jun 2020 08:33:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2011718/SRX2011718.20_model.r WARNING @ Tue, 16 Jun 2020 08:33:41: #2 Since the d (173) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:33:41: #2 You may need to consider one of the other alternative d(s): 173 WARNING @ Tue, 16 Jun 2020 08:33:41: #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 08:33:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:33:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:33:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2011718/SRX2011718.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:33:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2011718/SRX2011718.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:33:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2011718/SRX2011718.10_summits.bed INFO @ Tue, 16 Jun 2020 08:33:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (260 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:33:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:34:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2011718/SRX2011718.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:34:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2011718/SRX2011718.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:34:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2011718/SRX2011718.20_summits.bed INFO @ Tue, 16 Jun 2020 08:34:04: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (177 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。