Job ID = 6366766 SRX = SRX2249332 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:59:23 prefetch.2.10.7: 1) Downloading 'SRR4427771'... 2020-06-15T22:59:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:01:25 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:01:25 prefetch.2.10.7: 1) 'SRR4427771' was downloaded successfully 2020-06-15T23:01:58 prefetch.2.10.7: 'SRR4427771' has 6 unresolved dependencies 2020-06-15T23:01:58 prefetch.2.10.7: 2) Downloading 'ncbi-acc:BX284601.4?vdb-ctx=refseq'... 2020-06-15T23:01:58 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:02:15 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:02:15 prefetch.2.10.7: 2) 'ncbi-acc:BX284601.4?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:02:15 prefetch.2.10.7: 3) Downloading 'ncbi-acc:BX284602.4?vdb-ctx=refseq'... 2020-06-15T23:02:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:02:30 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:02:30 prefetch.2.10.7: 3) 'ncbi-acc:BX284602.4?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:02:30 prefetch.2.10.7: 4) Downloading 'ncbi-acc:BX284603.3?vdb-ctx=refseq'... 2020-06-15T23:02:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:02:45 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:02:45 prefetch.2.10.7: 4) 'ncbi-acc:BX284603.3?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:02:45 prefetch.2.10.7: 5) Downloading 'ncbi-acc:BX284604.3?vdb-ctx=refseq'... 2020-06-15T23:02:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:03:01 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:03:01 prefetch.2.10.7: 5) 'ncbi-acc:BX284604.3?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:03:01 prefetch.2.10.7: 6) Downloading 'ncbi-acc:BX284605.4?vdb-ctx=refseq'... 2020-06-15T23:03:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:03:17 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:03:17 prefetch.2.10.7: 6) 'ncbi-acc:BX284605.4?vdb-ctx=refseq' was downloaded successfully 2020-06-15T23:03:17 prefetch.2.10.7: 7) Downloading 'ncbi-acc:BX284606.4?vdb-ctx=refseq'... 2020-06-15T23:03:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:03:33 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:03:33 prefetch.2.10.7: 7) 'ncbi-acc:BX284606.4?vdb-ctx=refseq' was downloaded successfully Read 30323524 spots for SRR4427771/SRR4427771.sra Written 30323524 spots for SRR4427771/SRR4427771.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: 00:10:50 30323524 reads; of these: 30323524 (100.00%) were unpaired; of these: 4754308 (15.68%) aligned 0 times 21348285 (70.40%) aligned exactly 1 time 4220931 (13.92%) aligned >1 times 84.32% overall alignment rate Time searching: 00:10:50 Overall time: 00:10:50 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] 4080300 / 25569216 = 0.1596 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 08:24:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2249332/SRX2249332.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2249332/SRX2249332.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2249332/SRX2249332.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2249332/SRX2249332.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 08:24:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:24:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:24:58: 1000000 INFO @ Tue, 16 Jun 2020 08:25:05: 2000000 INFO @ Tue, 16 Jun 2020 08:25:12: 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 @ Tue, 16 Jun 2020 08:25:19: 4000000 INFO @ Tue, 16 Jun 2020 08:25:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2249332/SRX2249332.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2249332/SRX2249332.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2249332/SRX2249332.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2249332/SRX2249332.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 08:25:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:25:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:25:26: 5000000 INFO @ Tue, 16 Jun 2020 08:25:28: 1000000 INFO @ Tue, 16 Jun 2020 08:25:34: 6000000 INFO @ Tue, 16 Jun 2020 08:25:35: 2000000 INFO @ Tue, 16 Jun 2020 08:25:42: 7000000 INFO @ Tue, 16 Jun 2020 08:25:43: 3000000 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 08:25:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2249332/SRX2249332.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2249332/SRX2249332.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2249332/SRX2249332.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2249332/SRX2249332.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 08:25:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:25:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:25:50: 8000000 INFO @ Tue, 16 Jun 2020 08:25:51: 4000000 INFO @ Tue, 16 Jun 2020 08:25:58: 1000000 INFO @ Tue, 16 Jun 2020 08:25:58: 9000000 INFO @ Tue, 16 Jun 2020 08:25:59: 5000000 INFO @ Tue, 16 Jun 2020 08:26:06: 2000000 INFO @ Tue, 16 Jun 2020 08:26:06: 10000000 INFO @ Tue, 16 Jun 2020 08:26:07: 6000000 INFO @ Tue, 16 Jun 2020 08:26:14: 3000000 INFO @ Tue, 16 Jun 2020 08:26:14: 11000000 INFO @ Tue, 16 Jun 2020 08:26:15: 7000000 INFO @ Tue, 16 Jun 2020 08:26:22: 12000000 INFO @ Tue, 16 Jun 2020 08:26:22: 4000000 INFO @ Tue, 16 Jun 2020 08:26:24: 8000000 INFO @ Tue, 16 Jun 2020 08:26:30: 13000000 INFO @ Tue, 16 Jun 2020 08:26:30: 5000000 INFO @ Tue, 16 Jun 2020 08:26:32: 9000000 INFO @ Tue, 16 Jun 2020 08:26:38: 6000000 INFO @ Tue, 16 Jun 2020 08:26:38: 14000000 INFO @ Tue, 16 Jun 2020 08:26:40: 10000000 INFO @ Tue, 16 Jun 2020 08:26:47: 15000000 INFO @ Tue, 16 Jun 2020 08:26:47: 7000000 INFO @ Tue, 16 Jun 2020 08:26:48: 11000000 INFO @ Tue, 16 Jun 2020 08:26:55: 16000000 INFO @ Tue, 16 Jun 2020 08:26:55: 8000000 INFO @ Tue, 16 Jun 2020 08:26:56: 12000000 INFO @ Tue, 16 Jun 2020 08:27:03: 17000000 INFO @ Tue, 16 Jun 2020 08:27:03: 9000000 INFO @ Tue, 16 Jun 2020 08:27:04: 13000000 INFO @ Tue, 16 Jun 2020 08:27:11: 18000000 INFO @ Tue, 16 Jun 2020 08:27:11: 10000000 INFO @ Tue, 16 Jun 2020 08:27:12: 14000000 INFO @ Tue, 16 Jun 2020 08:27:19: 19000000 INFO @ Tue, 16 Jun 2020 08:27:19: 11000000 INFO @ Tue, 16 Jun 2020 08:27:20: 15000000 INFO @ Tue, 16 Jun 2020 08:27:27: 20000000 INFO @ Tue, 16 Jun 2020 08:27:27: 12000000 INFO @ Tue, 16 Jun 2020 08:27:28: 16000000 INFO @ Tue, 16 Jun 2020 08:27:35: 21000000 INFO @ Tue, 16 Jun 2020 08:27:35: 13000000 INFO @ Tue, 16 Jun 2020 08:27:36: 17000000 INFO @ Tue, 16 Jun 2020 08:27:39: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:27:39: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:27:39: #1 total tags in treatment: 21488916 INFO @ Tue, 16 Jun 2020 08:27:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:27:39: #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 08:27:40: #1 tags after filtering in treatment: 21488916 INFO @ Tue, 16 Jun 2020 08:27:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:27:40: #1 finished! INFO @ Tue, 16 Jun 2020 08:27:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:27:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:27:41: #2 number of paired peaks: 179 WARNING @ Tue, 16 Jun 2020 08:27:41: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Tue, 16 Jun 2020 08:27:41: start model_add_line... INFO @ Tue, 16 Jun 2020 08:27:41: start X-correlation... INFO @ Tue, 16 Jun 2020 08:27:41: end of X-cor INFO @ Tue, 16 Jun 2020 08:27:41: #2 finished! INFO @ Tue, 16 Jun 2020 08:27:41: #2 predicted fragment length is 96 bps INFO @ Tue, 16 Jun 2020 08:27:41: #2 alternative fragment length(s) may be 2,84,96 bps INFO @ Tue, 16 Jun 2020 08:27:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2249332/SRX2249332.05_model.r WARNING @ Tue, 16 Jun 2020 08:27:41: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:27:41: #2 You may need to consider one of the other alternative d(s): 2,84,96 WARNING @ Tue, 16 Jun 2020 08:27:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:27:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:27:41: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:27:44: 14000000 INFO @ Tue, 16 Jun 2020 08:27:44: 18000000 INFO @ Tue, 16 Jun 2020 08:27:52: 15000000 INFO @ Tue, 16 Jun 2020 08:27:53: 19000000 INFO @ Tue, 16 Jun 2020 08:28:00: 16000000 INFO @ Tue, 16 Jun 2020 08:28:01: 20000000 INFO @ Tue, 16 Jun 2020 08:28:08: 17000000 INFO @ Tue, 16 Jun 2020 08:28:09: 21000000 INFO @ Tue, 16 Jun 2020 08:28:14: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:28:14: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:28:14: #1 total tags in treatment: 21488916 INFO @ Tue, 16 Jun 2020 08:28:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:28:14: #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 08:28:14: #1 tags after filtering in treatment: 21488916 INFO @ Tue, 16 Jun 2020 08:28:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:28:14: #1 finished! INFO @ Tue, 16 Jun 2020 08:28:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:28:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:28:16: #2 number of paired peaks: 179 WARNING @ Tue, 16 Jun 2020 08:28:16: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Tue, 16 Jun 2020 08:28:16: start model_add_line... INFO @ Tue, 16 Jun 2020 08:28:16: start X-correlation... INFO @ Tue, 16 Jun 2020 08:28:16: end of X-cor INFO @ Tue, 16 Jun 2020 08:28:16: #2 finished! INFO @ Tue, 16 Jun 2020 08:28:16: #2 predicted fragment length is 96 bps INFO @ Tue, 16 Jun 2020 08:28:16: #2 alternative fragment length(s) may be 2,84,96 bps INFO @ Tue, 16 Jun 2020 08:28:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2249332/SRX2249332.10_model.r WARNING @ Tue, 16 Jun 2020 08:28:16: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:28:16: #2 You may need to consider one of the other alternative d(s): 2,84,96 WARNING @ Tue, 16 Jun 2020 08:28:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:28:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:28:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:28:17: 18000000 INFO @ Tue, 16 Jun 2020 08:28:20: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:28:24: 19000000 INFO @ Tue, 16 Jun 2020 08:28:32: 20000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:28:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2249332/SRX2249332.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:28:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2249332/SRX2249332.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:28:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2249332/SRX2249332.05_summits.bed INFO @ Tue, 16 Jun 2020 08:28:39: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (564 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:28:39: 21000000 INFO @ Tue, 16 Jun 2020 08:28:43: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:28:43: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:28:43: #1 total tags in treatment: 21488916 INFO @ Tue, 16 Jun 2020 08:28:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:28:43: #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 08:28:43: #1 tags after filtering in treatment: 21488916 INFO @ Tue, 16 Jun 2020 08:28:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:28:43: #1 finished! INFO @ Tue, 16 Jun 2020 08:28:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:28:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:28:45: #2 number of paired peaks: 179 WARNING @ Tue, 16 Jun 2020 08:28:45: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Tue, 16 Jun 2020 08:28:45: start model_add_line... INFO @ Tue, 16 Jun 2020 08:28:45: start X-correlation... INFO @ Tue, 16 Jun 2020 08:28:45: end of X-cor INFO @ Tue, 16 Jun 2020 08:28:45: #2 finished! INFO @ Tue, 16 Jun 2020 08:28:45: #2 predicted fragment length is 96 bps INFO @ Tue, 16 Jun 2020 08:28:45: #2 alternative fragment length(s) may be 2,84,96 bps INFO @ Tue, 16 Jun 2020 08:28:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2249332/SRX2249332.20_model.r WARNING @ Tue, 16 Jun 2020 08:28:45: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:28:45: #2 You may need to consider one of the other alternative d(s): 2,84,96 WARNING @ Tue, 16 Jun 2020 08:28:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:28:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:28:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:28:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:29:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2249332/SRX2249332.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:29:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2249332/SRX2249332.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:29:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2249332/SRX2249332.10_summits.bed INFO @ Tue, 16 Jun 2020 08:29:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (403 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:29:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:29:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2249332/SRX2249332.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:29:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2249332/SRX2249332.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:29:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2249332/SRX2249332.20_summits.bed INFO @ Tue, 16 Jun 2020 08:29:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (242 records, 4 fields): 1 millis CompletedMACS2peakCalling