Job ID = 6497439 SRX = SRX494937 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T21:42:23 prefetch.2.10.7: 1) Downloading 'SRR1198469'... 2020-06-25T21:42:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T21:45:18 prefetch.2.10.7: HTTPS download succeed 2020-06-25T21:45:18 prefetch.2.10.7: 1) 'SRR1198469' was downloaded successfully Read 27599297 spots for SRR1198469/SRR1198469.sra Written 27599297 spots for SRR1198469/SRR1198469.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: 00:06:15 27599297 reads; of these: 27599297 (100.00%) were unpaired; of these: 1484643 (5.38%) aligned 0 times 21193709 (76.79%) aligned exactly 1 time 4920945 (17.83%) aligned >1 times 94.62% overall alignment rate Time searching: 00:06:15 Overall time: 00:06:15 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 12 files... [bam_rmdupse_core] 7997074 / 26114654 = 0.3062 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 07:01:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494937/SRX494937.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494937/SRX494937.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494937/SRX494937.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494937/SRX494937.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 07:01:32: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:01:32: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:01:39: 1000000 INFO @ Fri, 26 Jun 2020 07:01:47: 2000000 INFO @ Fri, 26 Jun 2020 07:01:55: 3000000 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 07:02:02: 4000000 INFO @ Fri, 26 Jun 2020 07:02:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494937/SRX494937.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494937/SRX494937.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494937/SRX494937.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494937/SRX494937.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 07:02:02: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:02:02: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:02:10: 1000000 INFO @ Fri, 26 Jun 2020 07:02:11: 5000000 INFO @ Fri, 26 Jun 2020 07:02:18: 2000000 INFO @ Fri, 26 Jun 2020 07:02:19: 6000000 INFO @ Fri, 26 Jun 2020 07:02:26: 3000000 INFO @ Fri, 26 Jun 2020 07:02:27: 7000000 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 07:02:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494937/SRX494937.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494937/SRX494937.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494937/SRX494937.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494937/SRX494937.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 07:02:32: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:02:32: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:02:34: 4000000 INFO @ Fri, 26 Jun 2020 07:02:35: 8000000 INFO @ Fri, 26 Jun 2020 07:02:41: 1000000 INFO @ Fri, 26 Jun 2020 07:02:43: 5000000 INFO @ Fri, 26 Jun 2020 07:02:44: 9000000 INFO @ Fri, 26 Jun 2020 07:02:49: 2000000 INFO @ Fri, 26 Jun 2020 07:02:52: 6000000 INFO @ Fri, 26 Jun 2020 07:02:53: 10000000 INFO @ Fri, 26 Jun 2020 07:02:58: 3000000 INFO @ Fri, 26 Jun 2020 07:03:00: 7000000 INFO @ Fri, 26 Jun 2020 07:03:01: 11000000 INFO @ Fri, 26 Jun 2020 07:03:06: 4000000 INFO @ Fri, 26 Jun 2020 07:03:08: 8000000 INFO @ Fri, 26 Jun 2020 07:03:10: 12000000 INFO @ Fri, 26 Jun 2020 07:03:14: 5000000 INFO @ Fri, 26 Jun 2020 07:03:17: 9000000 INFO @ Fri, 26 Jun 2020 07:03:18: 13000000 INFO @ Fri, 26 Jun 2020 07:03:22: 6000000 INFO @ Fri, 26 Jun 2020 07:03:24: 10000000 INFO @ Fri, 26 Jun 2020 07:03:25: 14000000 INFO @ Fri, 26 Jun 2020 07:03:30: 7000000 INFO @ Fri, 26 Jun 2020 07:03:32: 11000000 INFO @ Fri, 26 Jun 2020 07:03:33: 15000000 INFO @ Fri, 26 Jun 2020 07:03:37: 8000000 INFO @ Fri, 26 Jun 2020 07:03:40: 12000000 INFO @ Fri, 26 Jun 2020 07:03:40: 16000000 INFO @ Fri, 26 Jun 2020 07:03:44: 9000000 INFO @ Fri, 26 Jun 2020 07:03:47: 13000000 INFO @ Fri, 26 Jun 2020 07:03:48: 17000000 INFO @ Fri, 26 Jun 2020 07:03:52: 10000000 INFO @ Fri, 26 Jun 2020 07:03:54: 14000000 INFO @ Fri, 26 Jun 2020 07:03:55: 18000000 INFO @ Fri, 26 Jun 2020 07:03:56: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:03:56: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:03:56: #1 total tags in treatment: 18117580 INFO @ Fri, 26 Jun 2020 07:03:56: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:03:56: #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 07:03:57: #1 tags after filtering in treatment: 18117580 INFO @ Fri, 26 Jun 2020 07:03:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:03:57: #1 finished! INFO @ Fri, 26 Jun 2020 07:03:57: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:03:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:03:58: #2 number of paired peaks: 256 WARNING @ Fri, 26 Jun 2020 07:03:58: Fewer paired peaks (256) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 256 pairs to build model! INFO @ Fri, 26 Jun 2020 07:03:58: start model_add_line... INFO @ Fri, 26 Jun 2020 07:03:58: start X-correlation... INFO @ Fri, 26 Jun 2020 07:03:58: end of X-cor INFO @ Fri, 26 Jun 2020 07:03:58: #2 finished! INFO @ Fri, 26 Jun 2020 07:03:58: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:03:58: #2 alternative fragment length(s) may be 1,42 bps INFO @ Fri, 26 Jun 2020 07:03:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494937/SRX494937.05_model.r WARNING @ Fri, 26 Jun 2020 07:03:58: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:03:58: #2 You may need to consider one of the other alternative d(s): 1,42 WARNING @ Fri, 26 Jun 2020 07:03:58: #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 07:03:58: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:03:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:03:59: 11000000 INFO @ Fri, 26 Jun 2020 07:04:01: 15000000 INFO @ Fri, 26 Jun 2020 07:04:06: 12000000 INFO @ Fri, 26 Jun 2020 07:04:08: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:04:12: 13000000 INFO @ Fri, 26 Jun 2020 07:04:15: 17000000 INFO @ Fri, 26 Jun 2020 07:04:19: 14000000 INFO @ Fri, 26 Jun 2020 07:04:21: 18000000 INFO @ Fri, 26 Jun 2020 07:04:22: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:04:22: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:04:22: #1 total tags in treatment: 18117580 INFO @ Fri, 26 Jun 2020 07:04:22: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:04:22: #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 07:04:23: #1 tags after filtering in treatment: 18117580 INFO @ Fri, 26 Jun 2020 07:04:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:04:23: #1 finished! INFO @ Fri, 26 Jun 2020 07:04:23: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:04:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:04:24: #2 number of paired peaks: 256 WARNING @ Fri, 26 Jun 2020 07:04:24: Fewer paired peaks (256) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 256 pairs to build model! INFO @ Fri, 26 Jun 2020 07:04:24: start model_add_line... INFO @ Fri, 26 Jun 2020 07:04:24: start X-correlation... INFO @ Fri, 26 Jun 2020 07:04:24: end of X-cor INFO @ Fri, 26 Jun 2020 07:04:24: #2 finished! INFO @ Fri, 26 Jun 2020 07:04:24: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:04:24: #2 alternative fragment length(s) may be 1,42 bps INFO @ Fri, 26 Jun 2020 07:04:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494937/SRX494937.10_model.r INFO @ Fri, 26 Jun 2020 07:04:25: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:04:25: 15000000 WARNING @ Fri, 26 Jun 2020 07:04:29: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:04:29: #2 You may need to consider one of the other alternative d(s): 1,42 WARNING @ Fri, 26 Jun 2020 07:04:29: #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 07:04:29: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:04:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:04:31: 16000000 INFO @ Fri, 26 Jun 2020 07:04:37: 17000000 INFO @ Fri, 26 Jun 2020 07:04:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494937/SRX494937.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:04:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494937/SRX494937.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:04:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494937/SRX494937.05_summits.bed INFO @ Fri, 26 Jun 2020 07:04:37: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:04:43: 18000000 INFO @ Fri, 26 Jun 2020 07:04:44: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:04:44: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:04:44: #1 total tags in treatment: 18117580 INFO @ Fri, 26 Jun 2020 07:04:44: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:04:44: #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 07:04:44: #1 tags after filtering in treatment: 18117580 INFO @ Fri, 26 Jun 2020 07:04:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:04:44: #1 finished! INFO @ Fri, 26 Jun 2020 07:04:44: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:04:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:04:45: #2 number of paired peaks: 256 WARNING @ Fri, 26 Jun 2020 07:04:45: Fewer paired peaks (256) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 256 pairs to build model! INFO @ Fri, 26 Jun 2020 07:04:45: start model_add_line... INFO @ Fri, 26 Jun 2020 07:04:45: start X-correlation... INFO @ Fri, 26 Jun 2020 07:04:45: end of X-cor INFO @ Fri, 26 Jun 2020 07:04:45: #2 finished! INFO @ Fri, 26 Jun 2020 07:04:45: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:04:45: #2 alternative fragment length(s) may be 1,42 bps INFO @ Fri, 26 Jun 2020 07:04:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494937/SRX494937.20_model.r WARNING @ Fri, 26 Jun 2020 07:04:45: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:04:45: #2 You may need to consider one of the other alternative d(s): 1,42 WARNING @ Fri, 26 Jun 2020 07:04:45: #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 07:04:45: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:04:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:04:56: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:05:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494937/SRX494937.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:05:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494937/SRX494937.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:05:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494937/SRX494937.10_summits.bed INFO @ Fri, 26 Jun 2020 07:05:08: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:05:12: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:05:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494937/SRX494937.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:05:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494937/SRX494937.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:05:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494937/SRX494937.20_summits.bed INFO @ Fri, 26 Jun 2020 07:05:42: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling