Job ID = 6366717 SRX = SRX2228871 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:55:14 prefetch.2.10.7: 1) Downloading 'SRR4380327'... 2020-06-15T22:55:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:57:03 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:57:03 prefetch.2.10.7: 1) 'SRR4380327' was downloaded successfully Read 18247478 spots for SRR4380327/SRR4380327.sra Written 18247478 spots for SRR4380327/SRR4380327.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: 00:04:14 18247478 reads; of these: 18247478 (100.00%) were unpaired; of these: 278548 (1.53%) aligned 0 times 14787081 (81.04%) aligned exactly 1 time 3181849 (17.44%) aligned >1 times 98.47% overall alignment rate Time searching: 00:04:14 Overall time: 00:04:14 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] 1734305 / 17968930 = 0.0965 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 08:07:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228871/SRX2228871.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228871/SRX2228871.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228871/SRX2228871.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228871/SRX2228871.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 08:07:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:07:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:07:11: 1000000 INFO @ Tue, 16 Jun 2020 08:07:17: 2000000 INFO @ Tue, 16 Jun 2020 08:07:24: 3000000 INFO @ Tue, 16 Jun 2020 08:07:30: 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 08:07:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228871/SRX2228871.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228871/SRX2228871.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228871/SRX2228871.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228871/SRX2228871.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 08:07:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:07:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:07:36: 5000000 INFO @ Tue, 16 Jun 2020 08:07:42: 1000000 INFO @ Tue, 16 Jun 2020 08:07:43: 6000000 INFO @ Tue, 16 Jun 2020 08:07:49: 2000000 INFO @ Tue, 16 Jun 2020 08:07:50: 7000000 INFO @ Tue, 16 Jun 2020 08:07:56: 3000000 INFO @ Tue, 16 Jun 2020 08:07:57: 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 @ Tue, 16 Jun 2020 08:08:04: 4000000 INFO @ Tue, 16 Jun 2020 08:08:04: 9000000 INFO @ Tue, 16 Jun 2020 08:08:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228871/SRX2228871.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228871/SRX2228871.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228871/SRX2228871.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228871/SRX2228871.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 08:08:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:08:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:08:11: 5000000 INFO @ Tue, 16 Jun 2020 08:08:11: 10000000 INFO @ Tue, 16 Jun 2020 08:08:13: 1000000 INFO @ Tue, 16 Jun 2020 08:08:18: 6000000 INFO @ Tue, 16 Jun 2020 08:08:18: 11000000 INFO @ Tue, 16 Jun 2020 08:08:20: 2000000 INFO @ Tue, 16 Jun 2020 08:08:25: 7000000 INFO @ Tue, 16 Jun 2020 08:08:25: 12000000 INFO @ Tue, 16 Jun 2020 08:08:27: 3000000 INFO @ Tue, 16 Jun 2020 08:08:32: 8000000 INFO @ Tue, 16 Jun 2020 08:08:33: 13000000 INFO @ Tue, 16 Jun 2020 08:08:35: 4000000 INFO @ Tue, 16 Jun 2020 08:08:39: 9000000 INFO @ Tue, 16 Jun 2020 08:08:40: 14000000 INFO @ Tue, 16 Jun 2020 08:08:42: 5000000 INFO @ Tue, 16 Jun 2020 08:08:46: 10000000 INFO @ Tue, 16 Jun 2020 08:08:47: 15000000 INFO @ Tue, 16 Jun 2020 08:08:49: 6000000 INFO @ Tue, 16 Jun 2020 08:08:54: 11000000 INFO @ Tue, 16 Jun 2020 08:08:54: 16000000 INFO @ Tue, 16 Jun 2020 08:08:56: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:08:56: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:08:56: #1 total tags in treatment: 16234625 INFO @ Tue, 16 Jun 2020 08:08:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:08:56: #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 08:08:56: 7000000 INFO @ Tue, 16 Jun 2020 08:08:56: #1 tags after filtering in treatment: 16234625 INFO @ Tue, 16 Jun 2020 08:08:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:08:56: #1 finished! INFO @ Tue, 16 Jun 2020 08:08:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:08:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:08:57: #2 number of paired peaks: 221 WARNING @ Tue, 16 Jun 2020 08:08:57: Fewer paired peaks (221) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 221 pairs to build model! INFO @ Tue, 16 Jun 2020 08:08:57: start model_add_line... INFO @ Tue, 16 Jun 2020 08:08:57: start X-correlation... INFO @ Tue, 16 Jun 2020 08:08:57: end of X-cor INFO @ Tue, 16 Jun 2020 08:08:57: #2 finished! INFO @ Tue, 16 Jun 2020 08:08:57: #2 predicted fragment length is 46 bps INFO @ Tue, 16 Jun 2020 08:08:57: #2 alternative fragment length(s) may be 2,46,511 bps INFO @ Tue, 16 Jun 2020 08:08:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228871/SRX2228871.05_model.r WARNING @ Tue, 16 Jun 2020 08:08:57: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:08:57: #2 You may need to consider one of the other alternative d(s): 2,46,511 WARNING @ Tue, 16 Jun 2020 08:08:57: #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 08:08:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:08:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:09:01: 12000000 INFO @ Tue, 16 Jun 2020 08:09:03: 8000000 INFO @ Tue, 16 Jun 2020 08:09:08: 13000000 INFO @ Tue, 16 Jun 2020 08:09:10: 9000000 INFO @ Tue, 16 Jun 2020 08:09:14: 14000000 INFO @ Tue, 16 Jun 2020 08:09:17: 10000000 INFO @ Tue, 16 Jun 2020 08:09:22: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:09:24: 11000000 INFO @ Tue, 16 Jun 2020 08:09:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:09:29: 16000000 INFO @ Tue, 16 Jun 2020 08:09:30: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:09:30: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:09:30: #1 total tags in treatment: 16234625 INFO @ Tue, 16 Jun 2020 08:09:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:09:30: #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 08:09:31: #1 tags after filtering in treatment: 16234625 INFO @ Tue, 16 Jun 2020 08:09:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:09:31: #1 finished! INFO @ Tue, 16 Jun 2020 08:09:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:09:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:09:31: 12000000 INFO @ Tue, 16 Jun 2020 08:09:32: #2 number of paired peaks: 221 WARNING @ Tue, 16 Jun 2020 08:09:32: Fewer paired peaks (221) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 221 pairs to build model! INFO @ Tue, 16 Jun 2020 08:09:32: start model_add_line... INFO @ Tue, 16 Jun 2020 08:09:32: start X-correlation... INFO @ Tue, 16 Jun 2020 08:09:32: end of X-cor INFO @ Tue, 16 Jun 2020 08:09:32: #2 finished! INFO @ Tue, 16 Jun 2020 08:09:32: #2 predicted fragment length is 46 bps INFO @ Tue, 16 Jun 2020 08:09:32: #2 alternative fragment length(s) may be 2,46,511 bps INFO @ Tue, 16 Jun 2020 08:09:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228871/SRX2228871.10_model.r WARNING @ Tue, 16 Jun 2020 08:09:32: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:09:32: #2 You may need to consider one of the other alternative d(s): 2,46,511 WARNING @ Tue, 16 Jun 2020 08:09:32: #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 08:09:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:09:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:09:38: 13000000 INFO @ Tue, 16 Jun 2020 08:09:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228871/SRX2228871.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:09:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228871/SRX2228871.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:09:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228871/SRX2228871.05_summits.bed INFO @ Tue, 16 Jun 2020 08:09:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (711 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:09:44: 14000000 INFO @ Tue, 16 Jun 2020 08:09:50: 15000000 INFO @ Tue, 16 Jun 2020 08:09:57: 16000000 INFO @ Tue, 16 Jun 2020 08:09:58: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:09:58: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:09:58: #1 total tags in treatment: 16234625 INFO @ Tue, 16 Jun 2020 08:09:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:09:58: #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 08:09:58: #1 tags after filtering in treatment: 16234625 INFO @ Tue, 16 Jun 2020 08:09:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:09:58: #1 finished! INFO @ Tue, 16 Jun 2020 08:09:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:09:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:10:00: #2 number of paired peaks: 221 WARNING @ Tue, 16 Jun 2020 08:10:00: Fewer paired peaks (221) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 221 pairs to build model! INFO @ Tue, 16 Jun 2020 08:10:00: start model_add_line... INFO @ Tue, 16 Jun 2020 08:10:00: start X-correlation... INFO @ Tue, 16 Jun 2020 08:10:00: end of X-cor INFO @ Tue, 16 Jun 2020 08:10:00: #2 finished! INFO @ Tue, 16 Jun 2020 08:10:00: #2 predicted fragment length is 46 bps INFO @ Tue, 16 Jun 2020 08:10:00: #2 alternative fragment length(s) may be 2,46,511 bps INFO @ Tue, 16 Jun 2020 08:10:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228871/SRX2228871.20_model.r WARNING @ Tue, 16 Jun 2020 08:10:00: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:10:00: #2 You may need to consider one of the other alternative d(s): 2,46,511 WARNING @ Tue, 16 Jun 2020 08:10:00: #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 08:10:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:10:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:10:02: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:10:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228871/SRX2228871.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:10:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228871/SRX2228871.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:10:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228871/SRX2228871.10_summits.bed INFO @ Tue, 16 Jun 2020 08:10:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (407 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:10:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:10:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228871/SRX2228871.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:10:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228871/SRX2228871.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:10:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228871/SRX2228871.20_summits.bed INFO @ Tue, 16 Jun 2020 08:10:44: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (150 records, 4 fields): 2 millis CompletedMACS2peakCalling