Job ID = 6527412 SRX = SRX494833 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:30:37 prefetch.2.10.7: 1) Downloading 'SRR1198365'... 2020-06-29T12:30:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:33:57 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:33:57 prefetch.2.10.7: 1) 'SRR1198365' was downloaded successfully Read 30788149 spots for SRR1198365/SRR1198365.sra Written 30788149 spots for SRR1198365/SRR1198365.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: 00:04:57 30788149 reads; of these: 30788149 (100.00%) were unpaired; of these: 171804 (0.56%) aligned 0 times 25273582 (82.09%) aligned exactly 1 time 5342763 (17.35%) aligned >1 times 99.44% overall alignment rate Time searching: 00:04:57 Overall time: 00:04:57 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] 4711065 / 30616345 = 0.1539 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 @ Mon, 29 Jun 2020 21:52:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494833/SRX494833.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494833/SRX494833.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494833/SRX494833.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494833/SRX494833.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 @ Mon, 29 Jun 2020 21:52:23: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:52:23: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:52:28: 1000000 INFO @ Mon, 29 Jun 2020 21:52:33: 2000000 INFO @ Mon, 29 Jun 2020 21:52:38: 3000000 INFO @ Mon, 29 Jun 2020 21:52:43: 4000000 INFO @ Mon, 29 Jun 2020 21:52:47: 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 @ Mon, 29 Jun 2020 21:52:52: 6000000 INFO @ Mon, 29 Jun 2020 21:52:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494833/SRX494833.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494833/SRX494833.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494833/SRX494833.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494833/SRX494833.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 @ Mon, 29 Jun 2020 21:52:53: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:52:53: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:52:57: 7000000 INFO @ Mon, 29 Jun 2020 21:52:58: 1000000 INFO @ Mon, 29 Jun 2020 21:53:02: 8000000 INFO @ Mon, 29 Jun 2020 21:53:03: 2000000 INFO @ Mon, 29 Jun 2020 21:53:07: 9000000 INFO @ Mon, 29 Jun 2020 21:53:08: 3000000 INFO @ Mon, 29 Jun 2020 21:53:12: 10000000 INFO @ Mon, 29 Jun 2020 21:53:13: 4000000 INFO @ Mon, 29 Jun 2020 21:53:17: 11000000 INFO @ Mon, 29 Jun 2020 21:53:18: 5000000 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 @ Mon, 29 Jun 2020 21:53:22: 12000000 INFO @ Mon, 29 Jun 2020 21:53:23: 6000000 INFO @ Mon, 29 Jun 2020 21:53:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494833/SRX494833.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494833/SRX494833.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494833/SRX494833.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494833/SRX494833.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 @ Mon, 29 Jun 2020 21:53:23: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:53:23: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:53:27: 13000000 INFO @ Mon, 29 Jun 2020 21:53:28: 7000000 INFO @ Mon, 29 Jun 2020 21:53:29: 1000000 INFO @ Mon, 29 Jun 2020 21:53:33: 14000000 INFO @ Mon, 29 Jun 2020 21:53:33: 8000000 INFO @ Mon, 29 Jun 2020 21:53:34: 2000000 INFO @ Mon, 29 Jun 2020 21:53:38: 15000000 INFO @ Mon, 29 Jun 2020 21:53:39: 9000000 INFO @ Mon, 29 Jun 2020 21:53:39: 3000000 INFO @ Mon, 29 Jun 2020 21:53:43: 16000000 INFO @ Mon, 29 Jun 2020 21:53:44: 10000000 INFO @ Mon, 29 Jun 2020 21:53:44: 4000000 INFO @ Mon, 29 Jun 2020 21:53:49: 17000000 INFO @ Mon, 29 Jun 2020 21:53:49: 11000000 INFO @ Mon, 29 Jun 2020 21:53:50: 5000000 INFO @ Mon, 29 Jun 2020 21:53:54: 18000000 INFO @ Mon, 29 Jun 2020 21:53:55: 12000000 INFO @ Mon, 29 Jun 2020 21:53:55: 6000000 INFO @ Mon, 29 Jun 2020 21:54:00: 19000000 INFO @ Mon, 29 Jun 2020 21:54:00: 13000000 INFO @ Mon, 29 Jun 2020 21:54:00: 7000000 INFO @ Mon, 29 Jun 2020 21:54:05: 20000000 INFO @ Mon, 29 Jun 2020 21:54:05: 14000000 INFO @ Mon, 29 Jun 2020 21:54:06: 8000000 INFO @ Mon, 29 Jun 2020 21:54:10: 21000000 INFO @ Mon, 29 Jun 2020 21:54:11: 15000000 INFO @ Mon, 29 Jun 2020 21:54:11: 9000000 INFO @ Mon, 29 Jun 2020 21:54:16: 22000000 INFO @ Mon, 29 Jun 2020 21:54:16: 10000000 INFO @ Mon, 29 Jun 2020 21:54:16: 16000000 INFO @ Mon, 29 Jun 2020 21:54:21: 23000000 INFO @ Mon, 29 Jun 2020 21:54:22: 11000000 INFO @ Mon, 29 Jun 2020 21:54:22: 17000000 INFO @ Mon, 29 Jun 2020 21:54:27: 24000000 INFO @ Mon, 29 Jun 2020 21:54:27: 12000000 INFO @ Mon, 29 Jun 2020 21:54:27: 18000000 INFO @ Mon, 29 Jun 2020 21:54:32: 25000000 INFO @ Mon, 29 Jun 2020 21:54:32: 13000000 INFO @ Mon, 29 Jun 2020 21:54:32: 19000000 INFO @ Mon, 29 Jun 2020 21:54:37: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 21:54:37: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 21:54:37: #1 total tags in treatment: 25905280 INFO @ Mon, 29 Jun 2020 21:54:37: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:54:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 21:54:37: #1 tags after filtering in treatment: 25905280 INFO @ Mon, 29 Jun 2020 21:54:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:54:37: #1 finished! INFO @ Mon, 29 Jun 2020 21:54:37: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:54:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:54:38: 20000000 INFO @ Mon, 29 Jun 2020 21:54:38: 14000000 INFO @ Mon, 29 Jun 2020 21:54:39: #2 number of paired peaks: 150 WARNING @ Mon, 29 Jun 2020 21:54:39: Fewer paired peaks (150) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 150 pairs to build model! INFO @ Mon, 29 Jun 2020 21:54:39: start model_add_line... INFO @ Mon, 29 Jun 2020 21:54:39: start X-correlation... INFO @ Mon, 29 Jun 2020 21:54:39: end of X-cor INFO @ Mon, 29 Jun 2020 21:54:39: #2 finished! INFO @ Mon, 29 Jun 2020 21:54:39: #2 predicted fragment length is 1 bps INFO @ Mon, 29 Jun 2020 21:54:39: #2 alternative fragment length(s) may be 1,30,197,450,492,569,584 bps INFO @ Mon, 29 Jun 2020 21:54:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494833/SRX494833.05_model.r WARNING @ Mon, 29 Jun 2020 21:54:39: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:54:39: #2 You may need to consider one of the other alternative d(s): 1,30,197,450,492,569,584 WARNING @ Mon, 29 Jun 2020 21:54:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 21:54:39: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:54:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:54:43: 21000000 INFO @ Mon, 29 Jun 2020 21:54:43: 15000000 INFO @ Mon, 29 Jun 2020 21:54:48: 22000000 INFO @ Mon, 29 Jun 2020 21:54:49: 16000000 INFO @ Mon, 29 Jun 2020 21:54:54: 23000000 INFO @ Mon, 29 Jun 2020 21:54:54: 17000000 INFO @ Mon, 29 Jun 2020 21:54:59: 24000000 INFO @ Mon, 29 Jun 2020 21:54:59: 18000000 INFO @ Mon, 29 Jun 2020 21:55:04: 25000000 INFO @ Mon, 29 Jun 2020 21:55:05: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 21:55:09: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 21:55:09: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 21:55:09: #1 total tags in treatment: 25905280 INFO @ Mon, 29 Jun 2020 21:55:09: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:55:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 21:55:09: #1 tags after filtering in treatment: 25905280 INFO @ Mon, 29 Jun 2020 21:55:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:55:09: #1 finished! INFO @ Mon, 29 Jun 2020 21:55:09: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:55:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:55:10: 20000000 INFO @ Mon, 29 Jun 2020 21:55:11: #2 number of paired peaks: 150 WARNING @ Mon, 29 Jun 2020 21:55:11: Fewer paired peaks (150) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 150 pairs to build model! INFO @ Mon, 29 Jun 2020 21:55:11: start model_add_line... INFO @ Mon, 29 Jun 2020 21:55:11: start X-correlation... INFO @ Mon, 29 Jun 2020 21:55:11: end of X-cor INFO @ Mon, 29 Jun 2020 21:55:11: #2 finished! INFO @ Mon, 29 Jun 2020 21:55:11: #2 predicted fragment length is 1 bps INFO @ Mon, 29 Jun 2020 21:55:11: #2 alternative fragment length(s) may be 1,30,197,450,492,569,584 bps INFO @ Mon, 29 Jun 2020 21:55:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494833/SRX494833.10_model.r WARNING @ Mon, 29 Jun 2020 21:55:11: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:55:11: #2 You may need to consider one of the other alternative d(s): 1,30,197,450,492,569,584 WARNING @ Mon, 29 Jun 2020 21:55:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 21:55:11: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:55:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:55:15: 21000000 INFO @ Mon, 29 Jun 2020 21:55:16: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 21:55:21: 22000000 INFO @ Mon, 29 Jun 2020 21:55:26: 23000000 INFO @ Mon, 29 Jun 2020 21:55:30: 24000000 INFO @ Mon, 29 Jun 2020 21:55:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494833/SRX494833.05_peaks.xls INFO @ Mon, 29 Jun 2020 21:55:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494833/SRX494833.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 21:55:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494833/SRX494833.05_summits.bed INFO @ Mon, 29 Jun 2020 21:55:34: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 21:55:35: 25000000 INFO @ Mon, 29 Jun 2020 21:55:40: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 21:55:40: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 21:55:40: #1 total tags in treatment: 25905280 INFO @ Mon, 29 Jun 2020 21:55:40: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:55:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 21:55:40: #1 tags after filtering in treatment: 25905280 INFO @ Mon, 29 Jun 2020 21:55:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:55:40: #1 finished! INFO @ Mon, 29 Jun 2020 21:55:40: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:55:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:55:42: #2 number of paired peaks: 150 WARNING @ Mon, 29 Jun 2020 21:55:42: Fewer paired peaks (150) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 150 pairs to build model! INFO @ Mon, 29 Jun 2020 21:55:42: start model_add_line... INFO @ Mon, 29 Jun 2020 21:55:42: start X-correlation... INFO @ Mon, 29 Jun 2020 21:55:42: end of X-cor INFO @ Mon, 29 Jun 2020 21:55:42: #2 finished! INFO @ Mon, 29 Jun 2020 21:55:42: #2 predicted fragment length is 1 bps INFO @ Mon, 29 Jun 2020 21:55:42: #2 alternative fragment length(s) may be 1,30,197,450,492,569,584 bps INFO @ Mon, 29 Jun 2020 21:55:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494833/SRX494833.20_model.r WARNING @ Mon, 29 Jun 2020 21:55:42: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:55:42: #2 You may need to consider one of the other alternative d(s): 1,30,197,450,492,569,584 WARNING @ Mon, 29 Jun 2020 21:55:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 21:55:42: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:55:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:55:50: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 21:56:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494833/SRX494833.10_peaks.xls INFO @ Mon, 29 Jun 2020 21:56:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494833/SRX494833.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 21:56:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494833/SRX494833.10_summits.bed INFO @ Mon, 29 Jun 2020 21:56:07: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 21:56:19: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 21:56:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494833/SRX494833.20_peaks.xls INFO @ Mon, 29 Jun 2020 21:56:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494833/SRX494833.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 21:56:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494833/SRX494833.20_summits.bed INFO @ Mon, 29 Jun 2020 21:56:37: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling