Job ID = 10165652 SRX = SRX7879259 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 30104381 spots for SRR11272874/SRR11272874.sra Written 30104381 spots for SRR11272874/SRR11272874.sra fastq に変換しました。 bowtie でマッピング中... Your job 10165893 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:13 30104381 reads; of these: 30104381 (100.00%) were unpaired; of these: 446560 (1.48%) aligned 0 times 24722082 (82.12%) aligned exactly 1 time 4935739 (16.40%) aligned >1 times 98.52% overall alignment rate Time searching: 00:07:13 Overall time: 00:07:13 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_rmdupse_core] 4396151 / 29657821 = 0.1482 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 @ Thu, 08 Oct 2020 19:46:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.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 @ Thu, 08 Oct 2020 19:46:59: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:46:59: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:47:05: 1000000 INFO @ Thu, 08 Oct 2020 19:47:12: 2000000 INFO @ Thu, 08 Oct 2020 19:47:18: 3000000 INFO @ Thu, 08 Oct 2020 19:47:25: 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 @ Thu, 08 Oct 2020 19:47:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.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 @ Thu, 08 Oct 2020 19:47:29: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:47:29: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:47:31: 5000000 INFO @ Thu, 08 Oct 2020 19:47:37: 1000000 INFO @ Thu, 08 Oct 2020 19:47:39: 6000000 INFO @ Thu, 08 Oct 2020 19:47:44: 2000000 INFO @ Thu, 08 Oct 2020 19:47:46: 7000000 INFO @ Thu, 08 Oct 2020 19:47:52: 3000000 INFO @ Thu, 08 Oct 2020 19:47:54: 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 @ Thu, 08 Oct 2020 19:47:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.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 @ Thu, 08 Oct 2020 19:47:59: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:47:59: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:47:59: 4000000 INFO @ Thu, 08 Oct 2020 19:48:01: 9000000 INFO @ Thu, 08 Oct 2020 19:48:06: 1000000 INFO @ Thu, 08 Oct 2020 19:48:07: 5000000 INFO @ Thu, 08 Oct 2020 19:48:09: 10000000 INFO @ Thu, 08 Oct 2020 19:48:13: 2000000 INFO @ Thu, 08 Oct 2020 19:48:14: 6000000 INFO @ Thu, 08 Oct 2020 19:48:16: 11000000 INFO @ Thu, 08 Oct 2020 19:48:20: 3000000 INFO @ Thu, 08 Oct 2020 19:48:22: 7000000 INFO @ Thu, 08 Oct 2020 19:48:24: 12000000 INFO @ Thu, 08 Oct 2020 19:48:27: 4000000 INFO @ Thu, 08 Oct 2020 19:48:29: 8000000 INFO @ Thu, 08 Oct 2020 19:48:32: 13000000 INFO @ Thu, 08 Oct 2020 19:48:34: 5000000 INFO @ Thu, 08 Oct 2020 19:48:37: 9000000 INFO @ Thu, 08 Oct 2020 19:48:40: 14000000 INFO @ Thu, 08 Oct 2020 19:48:41: 6000000 INFO @ Thu, 08 Oct 2020 19:48:45: 10000000 INFO @ Thu, 08 Oct 2020 19:48:47: 15000000 INFO @ Thu, 08 Oct 2020 19:48:48: 7000000 INFO @ Thu, 08 Oct 2020 19:48:53: 11000000 INFO @ Thu, 08 Oct 2020 19:48:55: 8000000 INFO @ Thu, 08 Oct 2020 19:48:55: 16000000 INFO @ Thu, 08 Oct 2020 19:49:01: 12000000 INFO @ Thu, 08 Oct 2020 19:49:02: 9000000 INFO @ Thu, 08 Oct 2020 19:49:03: 17000000 INFO @ Thu, 08 Oct 2020 19:49:09: 10000000 INFO @ Thu, 08 Oct 2020 19:49:09: 13000000 INFO @ Thu, 08 Oct 2020 19:49:10: 18000000 INFO @ Thu, 08 Oct 2020 19:49:16: 11000000 INFO @ Thu, 08 Oct 2020 19:49:17: 14000000 INFO @ Thu, 08 Oct 2020 19:49:18: 19000000 INFO @ Thu, 08 Oct 2020 19:49:23: 12000000 INFO @ Thu, 08 Oct 2020 19:49:24: 15000000 INFO @ Thu, 08 Oct 2020 19:49:25: 20000000 INFO @ Thu, 08 Oct 2020 19:49:31: 13000000 INFO @ Thu, 08 Oct 2020 19:49:32: 16000000 INFO @ Thu, 08 Oct 2020 19:49:33: 21000000 INFO @ Thu, 08 Oct 2020 19:49:38: 14000000 INFO @ Thu, 08 Oct 2020 19:49:40: 17000000 INFO @ Thu, 08 Oct 2020 19:49:40: 22000000 INFO @ Thu, 08 Oct 2020 19:49:45: 15000000 INFO @ Thu, 08 Oct 2020 19:49:47: 23000000 INFO @ Thu, 08 Oct 2020 19:49:47: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 19:49:52: 16000000 INFO @ Thu, 08 Oct 2020 19:49:54: 24000000 INFO @ Thu, 08 Oct 2020 19:49:55: 19000000 INFO @ Thu, 08 Oct 2020 19:49:59: 17000000 INFO @ Thu, 08 Oct 2020 19:50:01: 25000000 INFO @ Thu, 08 Oct 2020 19:50:02: 20000000 INFO @ Thu, 08 Oct 2020 19:50:03: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:50:03: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:50:03: #1 total tags in treatment: 25261670 INFO @ Thu, 08 Oct 2020 19:50:03: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:50:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 19:50:03: #1 tags after filtering in treatment: 25261670 INFO @ Thu, 08 Oct 2020 19:50:03: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:50:03: #1 finished! INFO @ Thu, 08 Oct 2020 19:50:03: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:50:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:50:05: #2 number of paired peaks: 146 WARNING @ Thu, 08 Oct 2020 19:50:05: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Thu, 08 Oct 2020 19:50:05: start model_add_line... INFO @ Thu, 08 Oct 2020 19:50:05: start X-correlation... INFO @ Thu, 08 Oct 2020 19:50:05: end of X-cor INFO @ Thu, 08 Oct 2020 19:50:05: #2 finished! INFO @ Thu, 08 Oct 2020 19:50:05: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 19:50:05: #2 alternative fragment length(s) may be 1,14,33,192,479,535,589,596 bps INFO @ Thu, 08 Oct 2020 19:50:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.05_model.r WARNING @ Thu, 08 Oct 2020 19:50:05: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:50:05: #2 You may need to consider one of the other alternative d(s): 1,14,33,192,479,535,589,596 WARNING @ Thu, 08 Oct 2020 19:50:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 19:50:05: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:50:05: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:50:06: 18000000 INFO @ Thu, 08 Oct 2020 19:50:10: 21000000 INFO @ Thu, 08 Oct 2020 19:50:13: 19000000 INFO @ Thu, 08 Oct 2020 19:50:17: 22000000 INFO @ Thu, 08 Oct 2020 19:50:20: 20000000 INFO @ Thu, 08 Oct 2020 19:50:24: 23000000 INFO @ Thu, 08 Oct 2020 19:50:26: 21000000 INFO @ Thu, 08 Oct 2020 19:50:31: 24000000 INFO @ Thu, 08 Oct 2020 19:50:33: 22000000 INFO @ Thu, 08 Oct 2020 19:50:39: 25000000 INFO @ Thu, 08 Oct 2020 19:50:40: 23000000 INFO @ Thu, 08 Oct 2020 19:50:40: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:50:40: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:50:40: #1 total tags in treatment: 25261670 INFO @ Thu, 08 Oct 2020 19:50:40: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:50:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 19:50:41: #1 tags after filtering in treatment: 25261670 INFO @ Thu, 08 Oct 2020 19:50:41: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:50:41: #1 finished! INFO @ Thu, 08 Oct 2020 19:50:41: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:50:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:50:41: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 19:50:42: #2 number of paired peaks: 146 WARNING @ Thu, 08 Oct 2020 19:50:42: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Thu, 08 Oct 2020 19:50:42: start model_add_line... INFO @ Thu, 08 Oct 2020 19:50:42: start X-correlation... INFO @ Thu, 08 Oct 2020 19:50:42: end of X-cor INFO @ Thu, 08 Oct 2020 19:50:42: #2 finished! INFO @ Thu, 08 Oct 2020 19:50:42: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 19:50:42: #2 alternative fragment length(s) may be 1,14,33,192,479,535,589,596 bps INFO @ Thu, 08 Oct 2020 19:50:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.10_model.r WARNING @ Thu, 08 Oct 2020 19:50:42: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:50:42: #2 You may need to consider one of the other alternative d(s): 1,14,33,192,479,535,589,596 WARNING @ Thu, 08 Oct 2020 19:50:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 19:50:42: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:50:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:50:46: 24000000 INFO @ Thu, 08 Oct 2020 19:50:53: 25000000 INFO @ Thu, 08 Oct 2020 19:50:54: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:50:54: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:50:54: #1 total tags in treatment: 25261670 INFO @ Thu, 08 Oct 2020 19:50:54: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:50:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 19:50:55: #1 tags after filtering in treatment: 25261670 INFO @ Thu, 08 Oct 2020 19:50:55: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:50:55: #1 finished! INFO @ Thu, 08 Oct 2020 19:50:55: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:50:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:50:56: #2 number of paired peaks: 146 WARNING @ Thu, 08 Oct 2020 19:50:56: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Thu, 08 Oct 2020 19:50:56: start model_add_line... INFO @ Thu, 08 Oct 2020 19:50:56: start X-correlation... INFO @ Thu, 08 Oct 2020 19:50:56: end of X-cor INFO @ Thu, 08 Oct 2020 19:50:56: #2 finished! INFO @ Thu, 08 Oct 2020 19:50:56: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 19:50:56: #2 alternative fragment length(s) may be 1,14,33,192,479,535,589,596 bps INFO @ Thu, 08 Oct 2020 19:50:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.20_model.r WARNING @ Thu, 08 Oct 2020 19:50:56: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:50:56: #2 You may need to consider one of the other alternative d(s): 1,14,33,192,479,535,589,596 WARNING @ Thu, 08 Oct 2020 19:50:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 19:50:56: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:50:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:50:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.05_peaks.xls INFO @ Thu, 08 Oct 2020 19:50:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:50:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.05_summits.bed INFO @ Thu, 08 Oct 2020 19:50:58: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 19:51:19: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:51:33: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:51:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.10_peaks.xls INFO @ Thu, 08 Oct 2020 19:51:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:51:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.10_summits.bed INFO @ Thu, 08 Oct 2020 19:51:36: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 19:51:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.20_peaks.xls INFO @ Thu, 08 Oct 2020 19:51:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:51:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7879259/SRX7879259.20_summits.bed INFO @ Thu, 08 Oct 2020 19:51:51: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling