Job ID = 6497478 SRX = SRX494979 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T21:54:44 prefetch.2.10.7: 1) Downloading 'SRR1198511'... 2020-06-25T21:54:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T21:56:08 prefetch.2.10.7: HTTPS download succeed 2020-06-25T21:56:09 prefetch.2.10.7: 'SRR1198511' is valid 2020-06-25T21:56:09 prefetch.2.10.7: 1) 'SRR1198511' was downloaded successfully Read 19310035 spots for SRR1198511/SRR1198511.sra Written 19310035 spots for SRR1198511/SRR1198511.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: 00:02:43 19310035 reads; of these: 19310035 (100.00%) were unpaired; of these: 1047755 (5.43%) aligned 0 times 14912155 (77.22%) aligned exactly 1 time 3350125 (17.35%) aligned >1 times 94.57% overall alignment rate Time searching: 00:02:43 Overall time: 00:02:43 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_rmdupse_core] 1735453 / 18262280 = 0.0950 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 07:03:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494979/SRX494979.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494979/SRX494979.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494979/SRX494979.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494979/SRX494979.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 07:03:44: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:03:44: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:03:49: 1000000 INFO @ Fri, 26 Jun 2020 07:03:55: 2000000 INFO @ Fri, 26 Jun 2020 07:04:00: 3000000 INFO @ Fri, 26 Jun 2020 07:04:05: 4000000 INFO @ Fri, 26 Jun 2020 07:04:11: 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 @ Fri, 26 Jun 2020 07:04:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494979/SRX494979.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494979/SRX494979.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494979/SRX494979.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494979/SRX494979.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 07:04:14: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:04:14: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:04:17: 6000000 INFO @ Fri, 26 Jun 2020 07:04:20: 1000000 INFO @ Fri, 26 Jun 2020 07:04:23: 7000000 INFO @ Fri, 26 Jun 2020 07:04:26: 2000000 INFO @ Fri, 26 Jun 2020 07:04:29: 8000000 INFO @ Fri, 26 Jun 2020 07:04:32: 3000000 INFO @ Fri, 26 Jun 2020 07:04:35: 9000000 INFO @ Fri, 26 Jun 2020 07:04:38: 4000000 INFO @ Fri, 26 Jun 2020 07:04:41: 10000000 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 07:04:44: 5000000 INFO @ Fri, 26 Jun 2020 07:04:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494979/SRX494979.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494979/SRX494979.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494979/SRX494979.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494979/SRX494979.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 07:04:45: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:04:45: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:04:47: 11000000 INFO @ Fri, 26 Jun 2020 07:04:50: 6000000 INFO @ Fri, 26 Jun 2020 07:04:51: 1000000 INFO @ Fri, 26 Jun 2020 07:04:53: 12000000 INFO @ Fri, 26 Jun 2020 07:04:56: 7000000 INFO @ Fri, 26 Jun 2020 07:04:57: 2000000 INFO @ Fri, 26 Jun 2020 07:04:59: 13000000 INFO @ Fri, 26 Jun 2020 07:05:02: 8000000 INFO @ Fri, 26 Jun 2020 07:05:03: 3000000 INFO @ Fri, 26 Jun 2020 07:05:05: 14000000 INFO @ Fri, 26 Jun 2020 07:05:08: 9000000 INFO @ Fri, 26 Jun 2020 07:05:09: 4000000 INFO @ Fri, 26 Jun 2020 07:05:11: 15000000 INFO @ Fri, 26 Jun 2020 07:05:15: 10000000 INFO @ Fri, 26 Jun 2020 07:05:16: 5000000 INFO @ Fri, 26 Jun 2020 07:05:17: 16000000 INFO @ Fri, 26 Jun 2020 07:05:21: 11000000 INFO @ Fri, 26 Jun 2020 07:05:21: #1 tag size is determined as 28 bps INFO @ Fri, 26 Jun 2020 07:05:21: #1 tag size = 28 INFO @ Fri, 26 Jun 2020 07:05:21: #1 total tags in treatment: 16526827 INFO @ Fri, 26 Jun 2020 07:05:21: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:05:21: #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 07:05:21: #1 tags after filtering in treatment: 16526827 INFO @ Fri, 26 Jun 2020 07:05:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:05:21: #1 finished! INFO @ Fri, 26 Jun 2020 07:05:21: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:05:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:05:22: 6000000 INFO @ Fri, 26 Jun 2020 07:05:22: #2 number of paired peaks: 272 WARNING @ Fri, 26 Jun 2020 07:05:22: Fewer paired peaks (272) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 272 pairs to build model! INFO @ Fri, 26 Jun 2020 07:05:22: start model_add_line... INFO @ Fri, 26 Jun 2020 07:05:22: start X-correlation... INFO @ Fri, 26 Jun 2020 07:05:22: end of X-cor INFO @ Fri, 26 Jun 2020 07:05:22: #2 finished! INFO @ Fri, 26 Jun 2020 07:05:22: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:05:22: #2 alternative fragment length(s) may be 1,17,512,545,548,553,563,565,581 bps INFO @ Fri, 26 Jun 2020 07:05:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494979/SRX494979.05_model.r INFO @ Fri, 26 Jun 2020 07:05:26: 12000000 INFO @ Fri, 26 Jun 2020 07:05:28: 7000000 INFO @ Fri, 26 Jun 2020 07:05:32: 13000000 INFO @ Fri, 26 Jun 2020 07:05:34: 8000000 INFO @ Fri, 26 Jun 2020 07:05:38: 14000000 INFO @ Fri, 26 Jun 2020 07:05:40: 9000000 WARNING @ Fri, 26 Jun 2020 07:05:42: #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 07:05:42: #2 You may need to consider one of the other alternative d(s): 1,17,512,545,548,553,563,565,581 WARNING @ Fri, 26 Jun 2020 07:05:42: #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 07:05:42: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:05:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:05:44: 15000000 INFO @ Fri, 26 Jun 2020 07:05:46: 10000000 INFO @ Fri, 26 Jun 2020 07:05:50: 16000000 INFO @ Fri, 26 Jun 2020 07:05:52: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:05:54: #1 tag size is determined as 28 bps INFO @ Fri, 26 Jun 2020 07:05:54: #1 tag size = 28 INFO @ Fri, 26 Jun 2020 07:05:54: #1 total tags in treatment: 16526827 INFO @ Fri, 26 Jun 2020 07:05:54: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:05:54: #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 07:05:54: #1 tags after filtering in treatment: 16526827 INFO @ Fri, 26 Jun 2020 07:05:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:05:54: #1 finished! INFO @ Fri, 26 Jun 2020 07:05:54: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:05:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:05:55: #2 number of paired peaks: 272 WARNING @ Fri, 26 Jun 2020 07:05:55: Fewer paired peaks (272) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 272 pairs to build model! INFO @ Fri, 26 Jun 2020 07:05:55: start model_add_line... INFO @ Fri, 26 Jun 2020 07:05:55: start X-correlation... INFO @ Fri, 26 Jun 2020 07:05:55: end of X-cor INFO @ Fri, 26 Jun 2020 07:05:55: #2 finished! INFO @ Fri, 26 Jun 2020 07:05:55: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:05:55: #2 alternative fragment length(s) may be 1,17,512,545,548,553,563,565,581 bps INFO @ Fri, 26 Jun 2020 07:05:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494979/SRX494979.10_model.r INFO @ Fri, 26 Jun 2020 07:05:58: 12000000 INFO @ Fri, 26 Jun 2020 07:06:03: 13000000 INFO @ Fri, 26 Jun 2020 07:06:08: 14000000 INFO @ Fri, 26 Jun 2020 07:06:10: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:06:14: 15000000 INFO @ Fri, 26 Jun 2020 07:06:19: 16000000 INFO @ Fri, 26 Jun 2020 07:06:22: #1 tag size is determined as 28 bps INFO @ Fri, 26 Jun 2020 07:06:22: #1 tag size = 28 INFO @ Fri, 26 Jun 2020 07:06:22: #1 total tags in treatment: 16526827 INFO @ Fri, 26 Jun 2020 07:06:22: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:06:22: #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 07:06:22: #1 tags after filtering in treatment: 16526827 INFO @ Fri, 26 Jun 2020 07:06:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:06:22: #1 finished! INFO @ Fri, 26 Jun 2020 07:06:22: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:06:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:06:23: #2 number of paired peaks: 272 WARNING @ Fri, 26 Jun 2020 07:06:23: Fewer paired peaks (272) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 272 pairs to build model! INFO @ Fri, 26 Jun 2020 07:06:23: start model_add_line... INFO @ Fri, 26 Jun 2020 07:06:23: start X-correlation... INFO @ Fri, 26 Jun 2020 07:06:23: end of X-cor INFO @ Fri, 26 Jun 2020 07:06:23: #2 finished! INFO @ Fri, 26 Jun 2020 07:06:23: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:06:23: #2 alternative fragment length(s) may be 1,17,512,545,548,553,563,565,581 bps INFO @ Fri, 26 Jun 2020 07:06:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494979/SRX494979.20_model.r INFO @ Fri, 26 Jun 2020 07:06:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494979/SRX494979.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:06:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494979/SRX494979.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:06:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494979/SRX494979.05_summits.bed INFO @ Fri, 26 Jun 2020 07:06:47: Done! WARNING @ Fri, 26 Jun 2020 07:06:47: #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 07:06:47: #2 You may need to consider one of the other alternative d(s): 1,17,512,545,548,553,563,565,581 WARNING @ Fri, 26 Jun 2020 07:06:47: #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 07:06:47: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:06:47: #3 Pre-compute pvalue-qvalue table... WARNING @ Fri, 26 Jun 2020 07:06:47: #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 07:06:47: #2 You may need to consider one of the other alternative d(s): 1,17,512,545,548,553,563,565,581 WARNING @ Fri, 26 Jun 2020 07:06:47: #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 07:06:47: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:06:47: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (0 chroms): 4 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:07:15: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:07:15: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:07:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494979/SRX494979.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:07:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494979/SRX494979.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:07:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494979/SRX494979.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:07:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494979/SRX494979.10_summits.bed INFO @ Fri, 26 Jun 2020 07:07:49: Done! INFO @ Fri, 26 Jun 2020 07:07:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494979/SRX494979.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:07:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494979/SRX494979.20_summits.bed INFO @ Fri, 26 Jun 2020 07:07:49: Done! BigWig に変換しました。 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling pass1 - making usageList (0 chroms): 6 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling