Job ID = 6367012 SRX = SRX2582951 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:12:16 prefetch.2.10.7: 1) Downloading 'SRR5279125'... 2020-06-15T23:12:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:13:20 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:13:21 prefetch.2.10.7: 'SRR5279125' is valid 2020-06-15T23:13:21 prefetch.2.10.7: 1) 'SRR5279125' was downloaded successfully 2020-06-15T23:13:21 prefetch.2.10.7: 'SRR5279125' has 0 unresolved dependencies Read 12852280 spots for SRR5279125/SRR5279125.sra Written 12852280 spots for SRR5279125/SRR5279125.sra 2020-06-15T23:14:17 prefetch.2.10.7: 1) Downloading 'SRR5279126'... 2020-06-15T23:14:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:15:15 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:15:16 prefetch.2.10.7: 'SRR5279126' is valid 2020-06-15T23:15:16 prefetch.2.10.7: 1) 'SRR5279126' was downloaded successfully 2020-06-15T23:15:16 prefetch.2.10.7: 'SRR5279126' has 0 unresolved dependencies Read 12484521 spots for SRR5279126/SRR5279126.sra Written 12484521 spots for SRR5279126/SRR5279126.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: 00:05:05 25336801 reads; of these: 25336801 (100.00%) were unpaired; of these: 3556328 (14.04%) aligned 0 times 18199147 (71.83%) aligned exactly 1 time 3581326 (14.13%) aligned >1 times 85.96% overall alignment rate Time searching: 00:05:05 Overall time: 00:05:05 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] 2264742 / 21780473 = 0.1040 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 08:26:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2582951/SRX2582951.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2582951/SRX2582951.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2582951/SRX2582951.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2582951/SRX2582951.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 08:26:13: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:26:13: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:26:20: 1000000 INFO @ Tue, 16 Jun 2020 08:26:27: 2000000 INFO @ Tue, 16 Jun 2020 08:26:33: 3000000 INFO @ Tue, 16 Jun 2020 08:26:40: 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 @ Tue, 16 Jun 2020 08:26:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2582951/SRX2582951.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2582951/SRX2582951.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2582951/SRX2582951.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2582951/SRX2582951.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 08:26:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:26:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:26:46: 5000000 INFO @ Tue, 16 Jun 2020 08:26:50: 1000000 INFO @ Tue, 16 Jun 2020 08:26:53: 6000000 INFO @ Tue, 16 Jun 2020 08:26:57: 2000000 INFO @ Tue, 16 Jun 2020 08:27:00: 7000000 INFO @ Tue, 16 Jun 2020 08:27:04: 3000000 INFO @ Tue, 16 Jun 2020 08:27:06: 8000000 INFO @ Tue, 16 Jun 2020 08:27:10: 4000000 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 08:27:13: 9000000 INFO @ Tue, 16 Jun 2020 08:27:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2582951/SRX2582951.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2582951/SRX2582951.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2582951/SRX2582951.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2582951/SRX2582951.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 08:27:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:27:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:27:17: 5000000 INFO @ Tue, 16 Jun 2020 08:27:20: 10000000 INFO @ Tue, 16 Jun 2020 08:27:21: 1000000 INFO @ Tue, 16 Jun 2020 08:27:24: 6000000 INFO @ Tue, 16 Jun 2020 08:27:27: 11000000 INFO @ Tue, 16 Jun 2020 08:27:28: 2000000 INFO @ Tue, 16 Jun 2020 08:27:30: 7000000 INFO @ Tue, 16 Jun 2020 08:27:33: 12000000 INFO @ Tue, 16 Jun 2020 08:27:35: 3000000 INFO @ Tue, 16 Jun 2020 08:27:37: 8000000 INFO @ Tue, 16 Jun 2020 08:27:40: 13000000 INFO @ Tue, 16 Jun 2020 08:27:41: 4000000 INFO @ Tue, 16 Jun 2020 08:27:44: 9000000 INFO @ Tue, 16 Jun 2020 08:27:47: 14000000 INFO @ Tue, 16 Jun 2020 08:27:48: 5000000 INFO @ Tue, 16 Jun 2020 08:27:51: 10000000 INFO @ Tue, 16 Jun 2020 08:27:54: 15000000 INFO @ Tue, 16 Jun 2020 08:27:55: 6000000 INFO @ Tue, 16 Jun 2020 08:27:58: 11000000 INFO @ Tue, 16 Jun 2020 08:28:01: 16000000 INFO @ Tue, 16 Jun 2020 08:28:02: 7000000 INFO @ Tue, 16 Jun 2020 08:28:05: 12000000 INFO @ Tue, 16 Jun 2020 08:28:08: 17000000 INFO @ Tue, 16 Jun 2020 08:28:09: 8000000 INFO @ Tue, 16 Jun 2020 08:28:12: 13000000 INFO @ Tue, 16 Jun 2020 08:28:14: 18000000 INFO @ Tue, 16 Jun 2020 08:28:16: 9000000 INFO @ Tue, 16 Jun 2020 08:28:19: 14000000 INFO @ Tue, 16 Jun 2020 08:28:21: 19000000 INFO @ Tue, 16 Jun 2020 08:28:23: 10000000 INFO @ Tue, 16 Jun 2020 08:28:25: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:28:25: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:28:25: #1 total tags in treatment: 19515731 INFO @ Tue, 16 Jun 2020 08:28:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:28:25: #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 08:28:25: #1 tags after filtering in treatment: 19515731 INFO @ Tue, 16 Jun 2020 08:28:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:28:25: #1 finished! INFO @ Tue, 16 Jun 2020 08:28:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:28:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:28:26: 15000000 INFO @ Tue, 16 Jun 2020 08:28:27: #2 number of paired peaks: 146 WARNING @ Tue, 16 Jun 2020 08:28:27: 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 @ Tue, 16 Jun 2020 08:28:27: start model_add_line... INFO @ Tue, 16 Jun 2020 08:28:27: start X-correlation... INFO @ Tue, 16 Jun 2020 08:28:27: end of X-cor INFO @ Tue, 16 Jun 2020 08:28:27: #2 finished! INFO @ Tue, 16 Jun 2020 08:28:27: #2 predicted fragment length is 45 bps INFO @ Tue, 16 Jun 2020 08:28:27: #2 alternative fragment length(s) may be 2,45,582 bps INFO @ Tue, 16 Jun 2020 08:28:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2582951/SRX2582951.05_model.r WARNING @ Tue, 16 Jun 2020 08:28:27: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:28:27: #2 You may need to consider one of the other alternative d(s): 2,45,582 WARNING @ Tue, 16 Jun 2020 08:28:27: #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 08:28:27: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:28:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:28:30: 11000000 INFO @ Tue, 16 Jun 2020 08:28:33: 16000000 INFO @ Tue, 16 Jun 2020 08:28:36: 12000000 INFO @ Tue, 16 Jun 2020 08:28:39: 17000000 INFO @ Tue, 16 Jun 2020 08:28:43: 13000000 INFO @ Tue, 16 Jun 2020 08:28:46: 18000000 INFO @ Tue, 16 Jun 2020 08:28:50: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:28:53: 19000000 INFO @ Tue, 16 Jun 2020 08:28:56: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:28:56: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:28:56: #1 total tags in treatment: 19515731 INFO @ Tue, 16 Jun 2020 08:28:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:28:56: #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 08:28:56: #1 tags after filtering in treatment: 19515731 INFO @ Tue, 16 Jun 2020 08:28:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:28:56: #1 finished! INFO @ Tue, 16 Jun 2020 08:28:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:28:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:28:57: 15000000 INFO @ Tue, 16 Jun 2020 08:28:58: #2 number of paired peaks: 146 WARNING @ Tue, 16 Jun 2020 08:28:58: 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 @ Tue, 16 Jun 2020 08:28:58: start model_add_line... INFO @ Tue, 16 Jun 2020 08:28:58: start X-correlation... INFO @ Tue, 16 Jun 2020 08:28:58: end of X-cor INFO @ Tue, 16 Jun 2020 08:28:58: #2 finished! INFO @ Tue, 16 Jun 2020 08:28:58: #2 predicted fragment length is 45 bps INFO @ Tue, 16 Jun 2020 08:28:58: #2 alternative fragment length(s) may be 2,45,582 bps INFO @ Tue, 16 Jun 2020 08:28:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2582951/SRX2582951.10_model.r WARNING @ Tue, 16 Jun 2020 08:28:58: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:28:58: #2 You may need to consider one of the other alternative d(s): 2,45,582 WARNING @ Tue, 16 Jun 2020 08:28:58: #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 08:28:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:28:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:29:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:29:04: 16000000 INFO @ Tue, 16 Jun 2020 08:29:10: 17000000 INFO @ Tue, 16 Jun 2020 08:29:17: 18000000 INFO @ Tue, 16 Jun 2020 08:29:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2582951/SRX2582951.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:29:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2582951/SRX2582951.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:29:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2582951/SRX2582951.05_summits.bed INFO @ Tue, 16 Jun 2020 08:29:17: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1551 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:29:23: 19000000 INFO @ Tue, 16 Jun 2020 08:29:26: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:29:26: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:29:26: #1 total tags in treatment: 19515731 INFO @ Tue, 16 Jun 2020 08:29:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:29:26: #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 08:29:27: #1 tags after filtering in treatment: 19515731 INFO @ Tue, 16 Jun 2020 08:29:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:29:27: #1 finished! INFO @ Tue, 16 Jun 2020 08:29:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:29:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:29:28: #2 number of paired peaks: 146 WARNING @ Tue, 16 Jun 2020 08:29:28: 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 @ Tue, 16 Jun 2020 08:29:28: start model_add_line... INFO @ Tue, 16 Jun 2020 08:29:28: start X-correlation... INFO @ Tue, 16 Jun 2020 08:29:28: end of X-cor INFO @ Tue, 16 Jun 2020 08:29:28: #2 finished! INFO @ Tue, 16 Jun 2020 08:29:28: #2 predicted fragment length is 45 bps INFO @ Tue, 16 Jun 2020 08:29:28: #2 alternative fragment length(s) may be 2,45,582 bps INFO @ Tue, 16 Jun 2020 08:29:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2582951/SRX2582951.20_model.r WARNING @ Tue, 16 Jun 2020 08:29:28: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:29:28: #2 You may need to consider one of the other alternative d(s): 2,45,582 WARNING @ Tue, 16 Jun 2020 08:29:28: #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 08:29:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:29:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:29:32: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:29:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2582951/SRX2582951.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:29:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2582951/SRX2582951.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:29:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2582951/SRX2582951.10_summits.bed INFO @ Tue, 16 Jun 2020 08:29:48: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (621 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:30:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:30:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2582951/SRX2582951.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:30:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2582951/SRX2582951.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:30:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2582951/SRX2582951.20_summits.bed INFO @ Tue, 16 Jun 2020 08:30:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (198 records, 4 fields): 1 millis CompletedMACS2peakCalling