Job ID = 6368916 SRX = SRX7175088 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-16T00:32:45 prefetch.2.10.7: 1) Downloading 'SRR10485520'... 2020-06-16T00:32:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:37:57 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:37:57 prefetch.2.10.7: 1) 'SRR10485520' was downloaded successfully 2020-06-16T00:37:57 prefetch.2.10.7: 'SRR10485520' has 0 unresolved dependencies Read 26256039 spots for SRR10485520/SRR10485520.sra Written 26256039 spots for SRR10485520/SRR10485520.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: 00:15:27 26256039 reads; of these: 26256039 (100.00%) were paired; of these: 11400538 (43.42%) aligned concordantly 0 times 12924444 (49.22%) aligned concordantly exactly 1 time 1931057 (7.35%) aligned concordantly >1 times ---- 11400538 pairs aligned concordantly 0 times; of these: 959478 (8.42%) aligned discordantly 1 time ---- 10441060 pairs aligned 0 times concordantly or discordantly; of these: 20882120 mates make up the pairs; of these: 19824094 (94.93%) aligned 0 times 674532 (3.23%) aligned exactly 1 time 383494 (1.84%) aligned >1 times 62.25% overall alignment rate Time searching: 00:15:27 Overall time: 00:15:27 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] 1238186 / 15794169 = 0.0784 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 10:04:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7175088/SRX7175088.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7175088/SRX7175088.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7175088/SRX7175088.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7175088/SRX7175088.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 10:04:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:04:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:04:56: 1000000 INFO @ Tue, 16 Jun 2020 10:05:01: 2000000 INFO @ Tue, 16 Jun 2020 10:05:06: 3000000 INFO @ Tue, 16 Jun 2020 10:05:10: 4000000 INFO @ Tue, 16 Jun 2020 10:05:15: 5000000 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 10:05:20: 6000000 INFO @ Tue, 16 Jun 2020 10:05:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7175088/SRX7175088.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7175088/SRX7175088.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7175088/SRX7175088.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7175088/SRX7175088.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 10:05:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:05:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:05:25: 7000000 INFO @ Tue, 16 Jun 2020 10:05:27: 1000000 INFO @ Tue, 16 Jun 2020 10:05:30: 8000000 INFO @ Tue, 16 Jun 2020 10:05:32: 2000000 INFO @ Tue, 16 Jun 2020 10:05:34: 9000000 INFO @ Tue, 16 Jun 2020 10:05:37: 3000000 INFO @ Tue, 16 Jun 2020 10:05:39: 10000000 INFO @ Tue, 16 Jun 2020 10:05:43: 4000000 INFO @ Tue, 16 Jun 2020 10:05:44: 11000000 INFO @ Tue, 16 Jun 2020 10:05:48: 5000000 INFO @ Tue, 16 Jun 2020 10:05:49: 12000000 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 10:05:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7175088/SRX7175088.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7175088/SRX7175088.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7175088/SRX7175088.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7175088/SRX7175088.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 10:05:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:05:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:05:53: 6000000 INFO @ Tue, 16 Jun 2020 10:05:54: 13000000 INFO @ Tue, 16 Jun 2020 10:05:56: 1000000 INFO @ Tue, 16 Jun 2020 10:05:59: 7000000 INFO @ Tue, 16 Jun 2020 10:05:59: 14000000 INFO @ Tue, 16 Jun 2020 10:06:01: 2000000 INFO @ Tue, 16 Jun 2020 10:06:04: 15000000 INFO @ Tue, 16 Jun 2020 10:06:04: 8000000 INFO @ Tue, 16 Jun 2020 10:06:06: 3000000 INFO @ Tue, 16 Jun 2020 10:06:09: 16000000 INFO @ Tue, 16 Jun 2020 10:06:09: 9000000 INFO @ Tue, 16 Jun 2020 10:06:10: 4000000 INFO @ Tue, 16 Jun 2020 10:06:14: 17000000 INFO @ Tue, 16 Jun 2020 10:06:15: 10000000 INFO @ Tue, 16 Jun 2020 10:06:15: 5000000 INFO @ Tue, 16 Jun 2020 10:06:18: 18000000 INFO @ Tue, 16 Jun 2020 10:06:20: 6000000 INFO @ Tue, 16 Jun 2020 10:06:20: 11000000 INFO @ Tue, 16 Jun 2020 10:06:23: 19000000 INFO @ Tue, 16 Jun 2020 10:06:25: 7000000 INFO @ Tue, 16 Jun 2020 10:06:25: 12000000 INFO @ Tue, 16 Jun 2020 10:06:28: 20000000 INFO @ Tue, 16 Jun 2020 10:06:29: 8000000 INFO @ Tue, 16 Jun 2020 10:06:31: 13000000 INFO @ Tue, 16 Jun 2020 10:06:33: 21000000 INFO @ Tue, 16 Jun 2020 10:06:34: 9000000 INFO @ Tue, 16 Jun 2020 10:06:36: 14000000 INFO @ Tue, 16 Jun 2020 10:06:38: 22000000 INFO @ Tue, 16 Jun 2020 10:06:39: 10000000 INFO @ Tue, 16 Jun 2020 10:06:42: 15000000 INFO @ Tue, 16 Jun 2020 10:06:42: 23000000 INFO @ Tue, 16 Jun 2020 10:06:44: 11000000 INFO @ Tue, 16 Jun 2020 10:06:47: 16000000 INFO @ Tue, 16 Jun 2020 10:06:47: 24000000 INFO @ Tue, 16 Jun 2020 10:06:49: 12000000 INFO @ Tue, 16 Jun 2020 10:06:52: 25000000 INFO @ Tue, 16 Jun 2020 10:06:53: 17000000 INFO @ Tue, 16 Jun 2020 10:06:54: 13000000 INFO @ Tue, 16 Jun 2020 10:06:57: 26000000 INFO @ Tue, 16 Jun 2020 10:06:58: 18000000 INFO @ Tue, 16 Jun 2020 10:06:59: 14000000 INFO @ Tue, 16 Jun 2020 10:07:02: 27000000 INFO @ Tue, 16 Jun 2020 10:07:03: 19000000 INFO @ Tue, 16 Jun 2020 10:07:04: 15000000 INFO @ Tue, 16 Jun 2020 10:07:07: 28000000 INFO @ Tue, 16 Jun 2020 10:07:08: 16000000 INFO @ Tue, 16 Jun 2020 10:07:09: 20000000 INFO @ Tue, 16 Jun 2020 10:07:11: 29000000 INFO @ Tue, 16 Jun 2020 10:07:13: 17000000 INFO @ Tue, 16 Jun 2020 10:07:14: 21000000 INFO @ Tue, 16 Jun 2020 10:07:16: 30000000 INFO @ Tue, 16 Jun 2020 10:07:17: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 10:07:17: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 10:07:17: #1 total tags in treatment: 13665099 INFO @ Tue, 16 Jun 2020 10:07:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:07:17: #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 10:07:18: #1 tags after filtering in treatment: 12523992 INFO @ Tue, 16 Jun 2020 10:07:18: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 16 Jun 2020 10:07:18: #1 finished! INFO @ Tue, 16 Jun 2020 10:07:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:07:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:07:18: 18000000 INFO @ Tue, 16 Jun 2020 10:07:19: #2 number of paired peaks: 323 WARNING @ Tue, 16 Jun 2020 10:07:19: Fewer paired peaks (323) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 323 pairs to build model! INFO @ Tue, 16 Jun 2020 10:07:19: start model_add_line... INFO @ Tue, 16 Jun 2020 10:07:19: start X-correlation... INFO @ Tue, 16 Jun 2020 10:07:19: end of X-cor INFO @ Tue, 16 Jun 2020 10:07:19: #2 finished! INFO @ Tue, 16 Jun 2020 10:07:19: #2 predicted fragment length is 146 bps INFO @ Tue, 16 Jun 2020 10:07:19: #2 alternative fragment length(s) may be 4,146 bps INFO @ Tue, 16 Jun 2020 10:07:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7175088/SRX7175088.05_model.r INFO @ Tue, 16 Jun 2020 10:07:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:07:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:07:19: 22000000 INFO @ Tue, 16 Jun 2020 10:07:23: 19000000 INFO @ Tue, 16 Jun 2020 10:07:25: 23000000 INFO @ Tue, 16 Jun 2020 10:07:28: 20000000 INFO @ Tue, 16 Jun 2020 10:07:30: 24000000 INFO @ Tue, 16 Jun 2020 10:07:33: 21000000 INFO @ Tue, 16 Jun 2020 10:07:35: 25000000 INFO @ Tue, 16 Jun 2020 10:07:37: 22000000 INFO @ Tue, 16 Jun 2020 10:07:41: 26000000 INFO @ Tue, 16 Jun 2020 10:07:42: 23000000 INFO @ Tue, 16 Jun 2020 10:07:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:07:46: 27000000 INFO @ Tue, 16 Jun 2020 10:07:47: 24000000 INFO @ Tue, 16 Jun 2020 10:07:51: 28000000 INFO @ Tue, 16 Jun 2020 10:07:52: 25000000 INFO @ Tue, 16 Jun 2020 10:07:57: 29000000 INFO @ Tue, 16 Jun 2020 10:07:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7175088/SRX7175088.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:07:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7175088/SRX7175088.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:07:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7175088/SRX7175088.05_summits.bed INFO @ Tue, 16 Jun 2020 10:07:57: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (363 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:07:57: 26000000 INFO @ Tue, 16 Jun 2020 10:08:02: 27000000 INFO @ Tue, 16 Jun 2020 10:08:02: 30000000 INFO @ Tue, 16 Jun 2020 10:08:03: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 10:08:03: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 10:08:03: #1 total tags in treatment: 13665099 INFO @ Tue, 16 Jun 2020 10:08:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:08:03: #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 10:08:04: #1 tags after filtering in treatment: 12523992 INFO @ Tue, 16 Jun 2020 10:08:04: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 16 Jun 2020 10:08:04: #1 finished! INFO @ Tue, 16 Jun 2020 10:08:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:08:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:08:04: #2 number of paired peaks: 323 WARNING @ Tue, 16 Jun 2020 10:08:04: Fewer paired peaks (323) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 323 pairs to build model! INFO @ Tue, 16 Jun 2020 10:08:04: start model_add_line... INFO @ Tue, 16 Jun 2020 10:08:05: start X-correlation... INFO @ Tue, 16 Jun 2020 10:08:05: end of X-cor INFO @ Tue, 16 Jun 2020 10:08:05: #2 finished! INFO @ Tue, 16 Jun 2020 10:08:05: #2 predicted fragment length is 146 bps INFO @ Tue, 16 Jun 2020 10:08:05: #2 alternative fragment length(s) may be 4,146 bps INFO @ Tue, 16 Jun 2020 10:08:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7175088/SRX7175088.10_model.r INFO @ Tue, 16 Jun 2020 10:08:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:08:05: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:08:07: 28000000 INFO @ Tue, 16 Jun 2020 10:08:11: 29000000 INFO @ Tue, 16 Jun 2020 10:08:16: 30000000 INFO @ Tue, 16 Jun 2020 10:08:17: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 10:08:17: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 10:08:17: #1 total tags in treatment: 13665099 INFO @ Tue, 16 Jun 2020 10:08:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:08:17: #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 10:08:17: #1 tags after filtering in treatment: 12523992 INFO @ Tue, 16 Jun 2020 10:08:17: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 16 Jun 2020 10:08:17: #1 finished! INFO @ Tue, 16 Jun 2020 10:08:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:08:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:08:18: #2 number of paired peaks: 323 WARNING @ Tue, 16 Jun 2020 10:08:18: Fewer paired peaks (323) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 323 pairs to build model! INFO @ Tue, 16 Jun 2020 10:08:18: start model_add_line... INFO @ Tue, 16 Jun 2020 10:08:18: start X-correlation... INFO @ Tue, 16 Jun 2020 10:08:18: end of X-cor INFO @ Tue, 16 Jun 2020 10:08:18: #2 finished! INFO @ Tue, 16 Jun 2020 10:08:18: #2 predicted fragment length is 146 bps INFO @ Tue, 16 Jun 2020 10:08:18: #2 alternative fragment length(s) may be 4,146 bps INFO @ Tue, 16 Jun 2020 10:08:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7175088/SRX7175088.20_model.r INFO @ Tue, 16 Jun 2020 10:08:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:08:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:08:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:08:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7175088/SRX7175088.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:08:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7175088/SRX7175088.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:08:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7175088/SRX7175088.10_summits.bed INFO @ Tue, 16 Jun 2020 10:08:41: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (260 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:08:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:08:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7175088/SRX7175088.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:08:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7175088/SRX7175088.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:08:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7175088/SRX7175088.20_summits.bed INFO @ Tue, 16 Jun 2020 10:08:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (193 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。