Job ID = 6497352 SRX = SRX2011720 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T21:35:50 prefetch.2.10.7: 1) Downloading 'SRR4017962'... 2020-06-25T21:35:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T21:42:38 prefetch.2.10.7: HTTPS download succeed 2020-06-25T21:42:38 prefetch.2.10.7: 1) 'SRR4017962' was downloaded successfully Read 16373839 spots for SRR4017962/SRR4017962.sra Written 16373839 spots for SRR4017962/SRR4017962.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:27:01 16373839 reads; of these: 16373839 (100.00%) were paired; of these: 2046614 (12.50%) aligned concordantly 0 times 12332735 (75.32%) aligned concordantly exactly 1 time 1994490 (12.18%) aligned concordantly >1 times ---- 2046614 pairs aligned concordantly 0 times; of these: 1491946 (72.90%) aligned discordantly 1 time ---- 554668 pairs aligned 0 times concordantly or discordantly; of these: 1109336 mates make up the pairs; of these: 403630 (36.38%) aligned 0 times 330355 (29.78%) aligned exactly 1 time 375351 (33.84%) aligned >1 times 98.77% overall alignment rate Time searching: 00:27:05 Overall time: 00:27:05 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] 2411165 / 15679847 = 0.1538 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 07:28:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2011720/SRX2011720.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2011720/SRX2011720.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2011720/SRX2011720.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2011720/SRX2011720.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 07:28:08: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:28:08: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:28:15: 1000000 INFO @ Fri, 26 Jun 2020 07:28:22: 2000000 INFO @ Fri, 26 Jun 2020 07:28:28: 3000000 INFO @ Fri, 26 Jun 2020 07:28:35: 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 @ Fri, 26 Jun 2020 07:28:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2011720/SRX2011720.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2011720/SRX2011720.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2011720/SRX2011720.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2011720/SRX2011720.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 07:28:38: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:28:38: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:28:42: 5000000 INFO @ Fri, 26 Jun 2020 07:28:45: 1000000 INFO @ Fri, 26 Jun 2020 07:28:49: 6000000 INFO @ Fri, 26 Jun 2020 07:28:53: 2000000 INFO @ Fri, 26 Jun 2020 07:28:56: 7000000 INFO @ Fri, 26 Jun 2020 07:29:01: 3000000 INFO @ Fri, 26 Jun 2020 07:29:03: 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 @ Fri, 26 Jun 2020 07:29:08: 4000000 INFO @ Fri, 26 Jun 2020 07:29:10: 9000000 INFO @ Fri, 26 Jun 2020 07:29:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2011720/SRX2011720.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2011720/SRX2011720.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2011720/SRX2011720.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2011720/SRX2011720.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 07:29:11: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:29:11: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:29:16: 5000000 INFO @ Fri, 26 Jun 2020 07:29:16: 10000000 INFO @ Fri, 26 Jun 2020 07:29:19: 1000000 INFO @ Fri, 26 Jun 2020 07:29:24: 11000000 INFO @ Fri, 26 Jun 2020 07:29:25: 6000000 INFO @ Fri, 26 Jun 2020 07:29:28: 2000000 INFO @ Fri, 26 Jun 2020 07:29:32: 12000000 INFO @ Fri, 26 Jun 2020 07:29:34: 7000000 INFO @ Fri, 26 Jun 2020 07:29:38: 3000000 INFO @ Fri, 26 Jun 2020 07:29:41: 13000000 INFO @ Fri, 26 Jun 2020 07:29:44: 8000000 INFO @ Fri, 26 Jun 2020 07:29:47: 4000000 INFO @ Fri, 26 Jun 2020 07:29:49: 14000000 INFO @ Fri, 26 Jun 2020 07:29:53: 9000000 INFO @ Fri, 26 Jun 2020 07:29:56: 5000000 INFO @ Fri, 26 Jun 2020 07:29:57: 15000000 INFO @ Fri, 26 Jun 2020 07:30:02: 10000000 INFO @ Fri, 26 Jun 2020 07:30:05: 6000000 INFO @ Fri, 26 Jun 2020 07:30:05: 16000000 INFO @ Fri, 26 Jun 2020 07:30:10: 11000000 INFO @ Fri, 26 Jun 2020 07:30:13: 17000000 INFO @ Fri, 26 Jun 2020 07:30:13: 7000000 INFO @ Fri, 26 Jun 2020 07:30:19: 12000000 INFO @ Fri, 26 Jun 2020 07:30:21: 18000000 INFO @ Fri, 26 Jun 2020 07:30:22: 8000000 INFO @ Fri, 26 Jun 2020 07:30:28: 13000000 INFO @ Fri, 26 Jun 2020 07:30:30: 19000000 INFO @ Fri, 26 Jun 2020 07:30:32: 9000000 INFO @ Fri, 26 Jun 2020 07:30:37: 14000000 INFO @ Fri, 26 Jun 2020 07:30:39: 20000000 INFO @ Fri, 26 Jun 2020 07:30:41: 10000000 INFO @ Fri, 26 Jun 2020 07:30:47: 15000000 INFO @ Fri, 26 Jun 2020 07:30:47: 21000000 INFO @ Fri, 26 Jun 2020 07:30:50: 11000000 INFO @ Fri, 26 Jun 2020 07:30:56: 22000000 INFO @ Fri, 26 Jun 2020 07:30:56: 16000000 INFO @ Fri, 26 Jun 2020 07:31:00: 12000000 INFO @ Fri, 26 Jun 2020 07:31:04: 23000000 INFO @ Fri, 26 Jun 2020 07:31:06: 17000000 INFO @ Fri, 26 Jun 2020 07:31:09: 13000000 INFO @ Fri, 26 Jun 2020 07:31:13: 24000000 INFO @ Fri, 26 Jun 2020 07:31:15: 18000000 INFO @ Fri, 26 Jun 2020 07:31:19: 14000000 INFO @ Fri, 26 Jun 2020 07:31:21: 25000000 INFO @ Fri, 26 Jun 2020 07:31:25: 19000000 INFO @ Fri, 26 Jun 2020 07:31:29: 15000000 INFO @ Fri, 26 Jun 2020 07:31:30: 26000000 INFO @ Fri, 26 Jun 2020 07:31:34: 20000000 INFO @ Fri, 26 Jun 2020 07:31:39: 27000000 INFO @ Fri, 26 Jun 2020 07:31:40: 16000000 INFO @ Fri, 26 Jun 2020 07:31:43: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 07:31:43: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 07:31:43: #1 total tags in treatment: 11998166 INFO @ Fri, 26 Jun 2020 07:31:43: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:31:43: #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 07:31:43: #1 tags after filtering in treatment: 10906332 INFO @ Fri, 26 Jun 2020 07:31:43: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 26 Jun 2020 07:31:43: #1 finished! INFO @ Fri, 26 Jun 2020 07:31:43: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:31:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:31:44: 21000000 INFO @ Fri, 26 Jun 2020 07:31:44: #2 number of paired peaks: 354 WARNING @ Fri, 26 Jun 2020 07:31:44: Fewer paired peaks (354) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 354 pairs to build model! INFO @ Fri, 26 Jun 2020 07:31:44: start model_add_line... INFO @ Fri, 26 Jun 2020 07:31:44: start X-correlation... INFO @ Fri, 26 Jun 2020 07:31:44: end of X-cor INFO @ Fri, 26 Jun 2020 07:31:44: #2 finished! INFO @ Fri, 26 Jun 2020 07:31:44: #2 predicted fragment length is 167 bps INFO @ Fri, 26 Jun 2020 07:31:44: #2 alternative fragment length(s) may be 167 bps INFO @ Fri, 26 Jun 2020 07:31:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2011720/SRX2011720.05_model.r WARNING @ Fri, 26 Jun 2020 07:31:44: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:31:44: #2 You may need to consider one of the other alternative d(s): 167 WARNING @ Fri, 26 Jun 2020 07:31:44: #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 07:31:44: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:31:44: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:31:50: 17000000 INFO @ Fri, 26 Jun 2020 07:31:53: 22000000 INFO @ Fri, 26 Jun 2020 07:31:59: 18000000 INFO @ Fri, 26 Jun 2020 07:32:01: 23000000 INFO @ Fri, 26 Jun 2020 07:32:08: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:32:09: 19000000 INFO @ Fri, 26 Jun 2020 07:32:10: 24000000 INFO @ Fri, 26 Jun 2020 07:32:18: 25000000 INFO @ Fri, 26 Jun 2020 07:32:19: 20000000 INFO @ Fri, 26 Jun 2020 07:32:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2011720/SRX2011720.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:32:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2011720/SRX2011720.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:32:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2011720/SRX2011720.05_summits.bed INFO @ Fri, 26 Jun 2020 07:32:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (419 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:32:27: 26000000 INFO @ Fri, 26 Jun 2020 07:32:28: 21000000 INFO @ Fri, 26 Jun 2020 07:32:36: 27000000 INFO @ Fri, 26 Jun 2020 07:32:39: 22000000 INFO @ Fri, 26 Jun 2020 07:32:41: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 07:32:41: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 07:32:41: #1 total tags in treatment: 11998166 INFO @ Fri, 26 Jun 2020 07:32:41: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:32:41: #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 07:32:41: #1 tags after filtering in treatment: 10906332 INFO @ Fri, 26 Jun 2020 07:32:41: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 26 Jun 2020 07:32:41: #1 finished! INFO @ Fri, 26 Jun 2020 07:32:41: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:32:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:32:42: #2 number of paired peaks: 354 WARNING @ Fri, 26 Jun 2020 07:32:42: Fewer paired peaks (354) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 354 pairs to build model! INFO @ Fri, 26 Jun 2020 07:32:42: start model_add_line... INFO @ Fri, 26 Jun 2020 07:32:42: start X-correlation... INFO @ Fri, 26 Jun 2020 07:32:42: end of X-cor INFO @ Fri, 26 Jun 2020 07:32:42: #2 finished! INFO @ Fri, 26 Jun 2020 07:32:42: #2 predicted fragment length is 167 bps INFO @ Fri, 26 Jun 2020 07:32:42: #2 alternative fragment length(s) may be 167 bps INFO @ Fri, 26 Jun 2020 07:32:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2011720/SRX2011720.10_model.r WARNING @ Fri, 26 Jun 2020 07:32:42: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:32:42: #2 You may need to consider one of the other alternative d(s): 167 WARNING @ Fri, 26 Jun 2020 07:32:42: #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 07:32:42: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:32:42: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:32:49: 23000000 INFO @ Fri, 26 Jun 2020 07:32:59: 24000000 INFO @ Fri, 26 Jun 2020 07:33:06: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:33:09: 25000000 INFO @ Fri, 26 Jun 2020 07:33:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2011720/SRX2011720.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:33:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2011720/SRX2011720.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:33:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2011720/SRX2011720.10_summits.bed INFO @ Fri, 26 Jun 2020 07:33:19: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (311 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:33:19: 26000000 INFO @ Fri, 26 Jun 2020 07:33:28: 27000000 INFO @ Fri, 26 Jun 2020 07:33:33: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 07:33:33: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 07:33:33: #1 total tags in treatment: 11998166 INFO @ Fri, 26 Jun 2020 07:33:33: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:33:33: #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 07:33:33: #1 tags after filtering in treatment: 10906332 INFO @ Fri, 26 Jun 2020 07:33:33: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 26 Jun 2020 07:33:33: #1 finished! INFO @ Fri, 26 Jun 2020 07:33:33: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:33:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:33:34: #2 number of paired peaks: 354 WARNING @ Fri, 26 Jun 2020 07:33:34: Fewer paired peaks (354) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 354 pairs to build model! INFO @ Fri, 26 Jun 2020 07:33:34: start model_add_line... INFO @ Fri, 26 Jun 2020 07:33:34: start X-correlation... INFO @ Fri, 26 Jun 2020 07:33:34: end of X-cor INFO @ Fri, 26 Jun 2020 07:33:34: #2 finished! INFO @ Fri, 26 Jun 2020 07:33:34: #2 predicted fragment length is 167 bps INFO @ Fri, 26 Jun 2020 07:33:34: #2 alternative fragment length(s) may be 167 bps INFO @ Fri, 26 Jun 2020 07:33:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2011720/SRX2011720.20_model.r WARNING @ Fri, 26 Jun 2020 07:33:39: #2 Since the d (167) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:33:39: #2 You may need to consider one of the other alternative d(s): 167 WARNING @ Fri, 26 Jun 2020 07:33:39: #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 07:33:39: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:33:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:34:05: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:34:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2011720/SRX2011720.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:34:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2011720/SRX2011720.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:34:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2011720/SRX2011720.20_summits.bed INFO @ Fri, 26 Jun 2020 07:34:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (214 records, 4 fields): 2 millis CompletedMACS2peakCalling