Job ID = 6367910 SRX = SRX4194203 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:36:47 prefetch.2.10.7: 1) Downloading 'SRR7291500'... 2020-06-15T23:36:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:38:16 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:38:16 prefetch.2.10.7: 'SRR7291500' is valid 2020-06-15T23:38:16 prefetch.2.10.7: 1) 'SRR7291500' was downloaded successfully 2020-06-15T23:38:16 prefetch.2.10.7: 'SRR7291500' has 0 unresolved dependencies Read 5982195 spots for SRR7291500/SRR7291500.sra Written 5982195 spots for SRR7291500/SRR7291500.sra 2020-06-15T23:38:55 prefetch.2.10.7: 1) Downloading 'SRR7291501'... 2020-06-15T23:38:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:40:21 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:40:22 prefetch.2.10.7: 'SRR7291501' is valid 2020-06-15T23:40:22 prefetch.2.10.7: 1) 'SRR7291501' was downloaded successfully 2020-06-15T23:40:22 prefetch.2.10.7: 'SRR7291501' has 0 unresolved dependencies Read 5864917 spots for SRR7291501/SRR7291501.sra Written 5864917 spots for SRR7291501/SRR7291501.sra 2020-06-15T23:40:57 prefetch.2.10.7: 1) Downloading 'SRR7291502'... 2020-06-15T23:40:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:41:56 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:41:56 prefetch.2.10.7: 'SRR7291502' is valid 2020-06-15T23:41:56 prefetch.2.10.7: 1) 'SRR7291502' was downloaded successfully 2020-06-15T23:41:56 prefetch.2.10.7: 'SRR7291502' has 0 unresolved dependencies Read 5977025 spots for SRR7291502/SRR7291502.sra Written 5977025 spots for SRR7291502/SRR7291502.sra 2020-06-15T23:42:35 prefetch.2.10.7: 1) Downloading 'SRR7291503'... 2020-06-15T23:42:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:43:25 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:43:25 prefetch.2.10.7: 'SRR7291503' is valid 2020-06-15T23:43:25 prefetch.2.10.7: 1) 'SRR7291503' was downloaded successfully 2020-06-15T23:43:25 prefetch.2.10.7: 'SRR7291503' has 0 unresolved dependencies Read 5790900 spots for SRR7291503/SRR7291503.sra Written 5790900 spots for SRR7291503/SRR7291503.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: 00:07:53 23615037 reads; of these: 23615037 (100.00%) were unpaired; of these: 328671 (1.39%) aligned 0 times 20222119 (85.63%) aligned exactly 1 time 3064247 (12.98%) aligned >1 times 98.61% overall alignment rate Time searching: 00:07:53 Overall time: 00:07:53 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] 6473064 / 23286366 = 0.2780 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 09:00:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194203/SRX4194203.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194203/SRX4194203.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194203/SRX4194203.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194203/SRX4194203.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 09:00:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:00:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:00:22: 1000000 INFO @ Tue, 16 Jun 2020 09:00:30: 2000000 INFO @ Tue, 16 Jun 2020 09:00:37: 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 09:00:44: 4000000 INFO @ Tue, 16 Jun 2020 09:00:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194203/SRX4194203.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194203/SRX4194203.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194203/SRX4194203.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194203/SRX4194203.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 09:00:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:00:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:00:51: 5000000 INFO @ Tue, 16 Jun 2020 09:00:52: 1000000 INFO @ Tue, 16 Jun 2020 09:00:58: 6000000 INFO @ Tue, 16 Jun 2020 09:00:59: 2000000 INFO @ Tue, 16 Jun 2020 09:01:06: 7000000 INFO @ Tue, 16 Jun 2020 09:01:07: 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 09:01:13: 8000000 INFO @ Tue, 16 Jun 2020 09:01:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194203/SRX4194203.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194203/SRX4194203.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194203/SRX4194203.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194203/SRX4194203.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 09:01:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:01:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:01:15: 4000000 INFO @ Tue, 16 Jun 2020 09:01:21: 9000000 INFO @ Tue, 16 Jun 2020 09:01:23: 1000000 INFO @ Tue, 16 Jun 2020 09:01:23: 5000000 INFO @ Tue, 16 Jun 2020 09:01:29: 10000000 INFO @ Tue, 16 Jun 2020 09:01:30: 2000000 INFO @ Tue, 16 Jun 2020 09:01:31: 6000000 INFO @ Tue, 16 Jun 2020 09:01:37: 11000000 INFO @ Tue, 16 Jun 2020 09:01:38: 3000000 INFO @ Tue, 16 Jun 2020 09:01:40: 7000000 INFO @ Tue, 16 Jun 2020 09:01:45: 12000000 INFO @ Tue, 16 Jun 2020 09:01:46: 4000000 INFO @ Tue, 16 Jun 2020 09:01:48: 8000000 INFO @ Tue, 16 Jun 2020 09:01:53: 13000000 INFO @ Tue, 16 Jun 2020 09:01:54: 5000000 INFO @ Tue, 16 Jun 2020 09:01:57: 9000000 INFO @ Tue, 16 Jun 2020 09:02:01: 14000000 INFO @ Tue, 16 Jun 2020 09:02:02: 6000000 INFO @ Tue, 16 Jun 2020 09:02:05: 10000000 INFO @ Tue, 16 Jun 2020 09:02:09: 15000000 INFO @ Tue, 16 Jun 2020 09:02:11: 7000000 INFO @ Tue, 16 Jun 2020 09:02:13: 11000000 INFO @ Tue, 16 Jun 2020 09:02:17: 16000000 INFO @ Tue, 16 Jun 2020 09:02:19: 8000000 INFO @ Tue, 16 Jun 2020 09:02:21: 12000000 INFO @ Tue, 16 Jun 2020 09:02:23: #1 tag size is determined as 65 bps INFO @ Tue, 16 Jun 2020 09:02:23: #1 tag size = 65 INFO @ Tue, 16 Jun 2020 09:02:23: #1 total tags in treatment: 16813302 INFO @ Tue, 16 Jun 2020 09:02:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:02:23: #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 09:02:23: #1 tags after filtering in treatment: 16813302 INFO @ Tue, 16 Jun 2020 09:02:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:02:23: #1 finished! INFO @ Tue, 16 Jun 2020 09:02:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:02:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:02:24: #2 number of paired peaks: 274 WARNING @ Tue, 16 Jun 2020 09:02:24: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Tue, 16 Jun 2020 09:02:24: start model_add_line... INFO @ Tue, 16 Jun 2020 09:02:25: start X-correlation... INFO @ Tue, 16 Jun 2020 09:02:25: end of X-cor INFO @ Tue, 16 Jun 2020 09:02:25: #2 finished! INFO @ Tue, 16 Jun 2020 09:02:25: #2 predicted fragment length is 67 bps INFO @ Tue, 16 Jun 2020 09:02:25: #2 alternative fragment length(s) may be 2,67,584 bps INFO @ Tue, 16 Jun 2020 09:02:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194203/SRX4194203.05_model.r WARNING @ Tue, 16 Jun 2020 09:02:25: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:02:25: #2 You may need to consider one of the other alternative d(s): 2,67,584 WARNING @ Tue, 16 Jun 2020 09:02:25: #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 09:02:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:02:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:02:26: 9000000 INFO @ Tue, 16 Jun 2020 09:02:29: 13000000 INFO @ Tue, 16 Jun 2020 09:02:34: 10000000 INFO @ Tue, 16 Jun 2020 09:02:37: 14000000 INFO @ Tue, 16 Jun 2020 09:02:41: 11000000 INFO @ Tue, 16 Jun 2020 09:02:44: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:02:48: 12000000 INFO @ Tue, 16 Jun 2020 09:02:52: 16000000 INFO @ Tue, 16 Jun 2020 09:02:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:02:55: 13000000 INFO @ Tue, 16 Jun 2020 09:02:58: #1 tag size is determined as 65 bps INFO @ Tue, 16 Jun 2020 09:02:58: #1 tag size = 65 INFO @ Tue, 16 Jun 2020 09:02:58: #1 total tags in treatment: 16813302 INFO @ Tue, 16 Jun 2020 09:02:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:02:58: #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 09:02:58: #1 tags after filtering in treatment: 16813302 INFO @ Tue, 16 Jun 2020 09:02:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:02:58: #1 finished! INFO @ Tue, 16 Jun 2020 09:02:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:02:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:02:59: #2 number of paired peaks: 274 WARNING @ Tue, 16 Jun 2020 09:02:59: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Tue, 16 Jun 2020 09:02:59: start model_add_line... INFO @ Tue, 16 Jun 2020 09:03:00: start X-correlation... INFO @ Tue, 16 Jun 2020 09:03:00: end of X-cor INFO @ Tue, 16 Jun 2020 09:03:00: #2 finished! INFO @ Tue, 16 Jun 2020 09:03:00: #2 predicted fragment length is 67 bps INFO @ Tue, 16 Jun 2020 09:03:00: #2 alternative fragment length(s) may be 2,67,584 bps INFO @ Tue, 16 Jun 2020 09:03:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194203/SRX4194203.10_model.r WARNING @ Tue, 16 Jun 2020 09:03:00: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:03:00: #2 You may need to consider one of the other alternative d(s): 2,67,584 WARNING @ Tue, 16 Jun 2020 09:03:00: #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 09:03:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:03:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:03:03: 14000000 INFO @ Tue, 16 Jun 2020 09:03:09: 15000000 INFO @ Tue, 16 Jun 2020 09:03:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194203/SRX4194203.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:03:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194203/SRX4194203.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:03:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194203/SRX4194203.05_summits.bed INFO @ Tue, 16 Jun 2020 09:03:10: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (6043 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:03:16: 16000000 INFO @ Tue, 16 Jun 2020 09:03:21: #1 tag size is determined as 65 bps INFO @ Tue, 16 Jun 2020 09:03:21: #1 tag size = 65 INFO @ Tue, 16 Jun 2020 09:03:21: #1 total tags in treatment: 16813302 INFO @ Tue, 16 Jun 2020 09:03:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:03:21: #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 09:03:21: #1 tags after filtering in treatment: 16813302 INFO @ Tue, 16 Jun 2020 09:03:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:03:21: #1 finished! INFO @ Tue, 16 Jun 2020 09:03:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:03:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:03:22: #2 number of paired peaks: 274 WARNING @ Tue, 16 Jun 2020 09:03:22: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Tue, 16 Jun 2020 09:03:22: start model_add_line... INFO @ Tue, 16 Jun 2020 09:03:23: start X-correlation... INFO @ Tue, 16 Jun 2020 09:03:23: end of X-cor INFO @ Tue, 16 Jun 2020 09:03:23: #2 finished! INFO @ Tue, 16 Jun 2020 09:03:23: #2 predicted fragment length is 67 bps INFO @ Tue, 16 Jun 2020 09:03:23: #2 alternative fragment length(s) may be 2,67,584 bps INFO @ Tue, 16 Jun 2020 09:03:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194203/SRX4194203.20_model.r WARNING @ Tue, 16 Jun 2020 09:03:23: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:03:23: #2 You may need to consider one of the other alternative d(s): 2,67,584 WARNING @ Tue, 16 Jun 2020 09:03:23: #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 09:03:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:03:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:03:29: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:03:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194203/SRX4194203.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:03:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194203/SRX4194203.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:03:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194203/SRX4194203.10_summits.bed INFO @ Tue, 16 Jun 2020 09:03:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1134 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:03:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:04:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194203/SRX4194203.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:04:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194203/SRX4194203.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:04:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194203/SRX4194203.20_summits.bed INFO @ Tue, 16 Jun 2020 09:04:05: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (211 records, 4 fields): 2 millis CompletedMACS2peakCalling