Job ID = 6367903 SRX = SRX4194196 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:46:32 prefetch.2.10.7: 1) Downloading 'SRR7291470'... 2020-06-15T23:46:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:47:27 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:47:28 prefetch.2.10.7: 'SRR7291470' is valid 2020-06-15T23:47:28 prefetch.2.10.7: 1) 'SRR7291470' was downloaded successfully 2020-06-15T23:47:28 prefetch.2.10.7: 'SRR7291470' has 0 unresolved dependencies Read 4376685 spots for SRR7291470/SRR7291470.sra Written 4376685 spots for SRR7291470/SRR7291470.sra 2020-06-15T23:47:55 prefetch.2.10.7: 1) Downloading 'SRR7291472'... 2020-06-15T23:47:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:48:50 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:48:50 prefetch.2.10.7: 'SRR7291472' is valid 2020-06-15T23:48:50 prefetch.2.10.7: 1) 'SRR7291472' was downloaded successfully 2020-06-15T23:48:50 prefetch.2.10.7: 'SRR7291472' has 0 unresolved dependencies Read 4283700 spots for SRR7291472/SRR7291472.sra Written 4283700 spots for SRR7291472/SRR7291472.sra 2020-06-15T23:49:20 prefetch.2.10.7: 1) Downloading 'SRR7291473'... 2020-06-15T23:49:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:50:00 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:50:00 prefetch.2.10.7: 'SRR7291473' is valid 2020-06-15T23:50:00 prefetch.2.10.7: 1) 'SRR7291473' was downloaded successfully 2020-06-15T23:50:00 prefetch.2.10.7: 'SRR7291473' has 0 unresolved dependencies Read 4375061 spots for SRR7291473/SRR7291473.sra Written 4375061 spots for SRR7291473/SRR7291473.sra 2020-06-15T23:50:30 prefetch.2.10.7: 1) Downloading 'SRR7291474'... 2020-06-15T23:50:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:51:12 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:51:13 prefetch.2.10.7: 'SRR7291474' is valid 2020-06-15T23:51:13 prefetch.2.10.7: 1) 'SRR7291474' was downloaded successfully 2020-06-15T23:51:13 prefetch.2.10.7: 'SRR7291474' has 0 unresolved dependencies Read 4232692 spots for SRR7291474/SRR7291474.sra Written 4232692 spots for SRR7291474/SRR7291474.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: 00:06:47 17268138 reads; of these: 17268138 (100.00%) were unpaired; of these: 499003 (2.89%) aligned 0 times 13407684 (77.64%) aligned exactly 1 time 3361451 (19.47%) aligned >1 times 97.11% overall alignment rate Time searching: 00:06:47 Overall time: 00:06:47 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] 4496326 / 16769135 = 0.2681 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 09:03:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194196/SRX4194196.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194196/SRX4194196.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194196/SRX4194196.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194196/SRX4194196.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 09:03:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:03:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:03:54: 1000000 INFO @ Tue, 16 Jun 2020 09:04:02: 2000000 INFO @ Tue, 16 Jun 2020 09:04:10: 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 09:04:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194196/SRX4194196.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194196/SRX4194196.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194196/SRX4194196.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194196/SRX4194196.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 09:04:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:04:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:04:19: 4000000 INFO @ Tue, 16 Jun 2020 09:04:24: 1000000 INFO @ Tue, 16 Jun 2020 09:04:28: 5000000 INFO @ Tue, 16 Jun 2020 09:04:32: 2000000 INFO @ Tue, 16 Jun 2020 09:04:36: 6000000 INFO @ Tue, 16 Jun 2020 09:04:40: 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 09:04:45: 7000000 INFO @ Tue, 16 Jun 2020 09:04:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194196/SRX4194196.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194196/SRX4194196.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194196/SRX4194196.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194196/SRX4194196.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 09:04:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:04:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:04:49: 4000000 INFO @ Tue, 16 Jun 2020 09:04:52: 8000000 INFO @ Tue, 16 Jun 2020 09:04:54: 1000000 INFO @ Tue, 16 Jun 2020 09:04:57: 5000000 INFO @ Tue, 16 Jun 2020 09:05:01: 9000000 INFO @ Tue, 16 Jun 2020 09:05:02: 2000000 INFO @ Tue, 16 Jun 2020 09:05:05: 6000000 INFO @ Tue, 16 Jun 2020 09:05:09: 10000000 INFO @ Tue, 16 Jun 2020 09:05:10: 3000000 INFO @ Tue, 16 Jun 2020 09:05:13: 7000000 INFO @ Tue, 16 Jun 2020 09:05:18: 11000000 INFO @ Tue, 16 Jun 2020 09:05:18: 4000000 INFO @ Tue, 16 Jun 2020 09:05:22: 8000000 INFO @ Tue, 16 Jun 2020 09:05:26: 5000000 INFO @ Tue, 16 Jun 2020 09:05:27: 12000000 INFO @ Tue, 16 Jun 2020 09:05:29: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 09:05:29: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 09:05:29: #1 total tags in treatment: 12272809 INFO @ Tue, 16 Jun 2020 09:05:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:05:29: #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 09:05:29: #1 tags after filtering in treatment: 12272809 INFO @ Tue, 16 Jun 2020 09:05:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:05:29: #1 finished! INFO @ Tue, 16 Jun 2020 09:05:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:05:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:05:30: #2 number of paired peaks: 444 WARNING @ Tue, 16 Jun 2020 09:05:30: Fewer paired peaks (444) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 444 pairs to build model! INFO @ Tue, 16 Jun 2020 09:05:30: start model_add_line... INFO @ Tue, 16 Jun 2020 09:05:30: start X-correlation... INFO @ Tue, 16 Jun 2020 09:05:30: end of X-cor INFO @ Tue, 16 Jun 2020 09:05:30: #2 finished! INFO @ Tue, 16 Jun 2020 09:05:30: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 09:05:30: #2 alternative fragment length(s) may be 3,51 bps INFO @ Tue, 16 Jun 2020 09:05:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194196/SRX4194196.05_model.r INFO @ Tue, 16 Jun 2020 09:05:30: 9000000 WARNING @ Tue, 16 Jun 2020 09:05:30: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:05:30: #2 You may need to consider one of the other alternative d(s): 3,51 WARNING @ Tue, 16 Jun 2020 09:05:30: #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 09:05:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:05:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:05:34: 6000000 INFO @ Tue, 16 Jun 2020 09:05:38: 10000000 INFO @ Tue, 16 Jun 2020 09:05:42: 7000000 INFO @ Tue, 16 Jun 2020 09:05:45: 11000000 INFO @ Tue, 16 Jun 2020 09:05:50: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:05:53: 12000000 INFO @ Tue, 16 Jun 2020 09:05:54: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 09:05:54: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 09:05:54: #1 total tags in treatment: 12272809 INFO @ Tue, 16 Jun 2020 09:05:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:05:54: #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 09:05:55: #1 tags after filtering in treatment: 12272809 INFO @ Tue, 16 Jun 2020 09:05:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:05:55: #1 finished! INFO @ Tue, 16 Jun 2020 09:05:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:05:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:05:56: #2 number of paired peaks: 444 WARNING @ Tue, 16 Jun 2020 09:05:56: Fewer paired peaks (444) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 444 pairs to build model! INFO @ Tue, 16 Jun 2020 09:05:56: start model_add_line... INFO @ Tue, 16 Jun 2020 09:05:56: start X-correlation... INFO @ Tue, 16 Jun 2020 09:05:56: end of X-cor INFO @ Tue, 16 Jun 2020 09:05:56: #2 finished! INFO @ Tue, 16 Jun 2020 09:05:56: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 09:05:56: #2 alternative fragment length(s) may be 3,51 bps INFO @ Tue, 16 Jun 2020 09:05:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194196/SRX4194196.10_model.r WARNING @ Tue, 16 Jun 2020 09:05:56: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:05:56: #2 You may need to consider one of the other alternative d(s): 3,51 WARNING @ Tue, 16 Jun 2020 09:05:56: #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 09:05:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:05:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:05:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:05:57: 9000000 INFO @ Tue, 16 Jun 2020 09:06:03: 10000000 INFO @ Tue, 16 Jun 2020 09:06:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194196/SRX4194196.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:06:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194196/SRX4194196.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:06:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194196/SRX4194196.05_summits.bed INFO @ Tue, 16 Jun 2020 09:06:10: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (651 records, 4 fields): 2 millis INFO @ Tue, 16 Jun 2020 09:06:10: 11000000 CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:06:16: 12000000 INFO @ Tue, 16 Jun 2020 09:06:18: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 09:06:18: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 09:06:18: #1 total tags in treatment: 12272809 INFO @ Tue, 16 Jun 2020 09:06:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:06:18: #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 09:06:18: #1 tags after filtering in treatment: 12272809 INFO @ Tue, 16 Jun 2020 09:06:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:06:18: #1 finished! INFO @ Tue, 16 Jun 2020 09:06:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:06:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:06:19: #2 number of paired peaks: 444 WARNING @ Tue, 16 Jun 2020 09:06:19: Fewer paired peaks (444) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 444 pairs to build model! INFO @ Tue, 16 Jun 2020 09:06:19: start model_add_line... INFO @ Tue, 16 Jun 2020 09:06:19: start X-correlation... INFO @ Tue, 16 Jun 2020 09:06:19: end of X-cor INFO @ Tue, 16 Jun 2020 09:06:19: #2 finished! INFO @ Tue, 16 Jun 2020 09:06:19: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 09:06:19: #2 alternative fragment length(s) may be 3,51 bps INFO @ Tue, 16 Jun 2020 09:06:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194196/SRX4194196.20_model.r WARNING @ Tue, 16 Jun 2020 09:06:19: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:06:19: #2 You may need to consider one of the other alternative d(s): 3,51 WARNING @ Tue, 16 Jun 2020 09:06:19: #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 09:06:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:06:19: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:06:20: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:06:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194196/SRX4194196.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:06:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194196/SRX4194196.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:06:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194196/SRX4194196.10_summits.bed INFO @ Tue, 16 Jun 2020 09:06:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (448 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:06:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:06:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194196/SRX4194196.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:06:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194196/SRX4194196.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:06:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194196/SRX4194196.20_summits.bed INFO @ Tue, 16 Jun 2020 09:06:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (199 records, 4 fields): 2 millis CompletedMACS2peakCalling