Job ID = 6497331 SRX = SRX1010109 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T21:20:29 prefetch.2.10.7: 1) Downloading 'SRR1998065'... 2020-06-25T21:20:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T21:25:16 prefetch.2.10.7: HTTPS download succeed 2020-06-25T21:25:16 prefetch.2.10.7: 1) 'SRR1998065' was downloaded successfully Read 12738894 spots for SRR1998065/SRR1998065.sra Written 12738894 spots for SRR1998065/SRR1998065.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: 00:00:01 Time loading mirror index: 00:00:02 Multiseed full-index search: 00:22:44 12738894 reads; of these: 12738894 (100.00%) were paired; of these: 270067 (2.12%) aligned concordantly 0 times 10844962 (85.13%) aligned concordantly exactly 1 time 1623865 (12.75%) aligned concordantly >1 times ---- 270067 pairs aligned concordantly 0 times; of these: 100510 (37.22%) aligned discordantly 1 time ---- 169557 pairs aligned 0 times concordantly or discordantly; of these: 339114 mates make up the pairs; of these: 154932 (45.69%) aligned 0 times 126983 (37.45%) aligned exactly 1 time 57199 (16.87%) aligned >1 times 99.39% overall alignment rate Time searching: 00:22:48 Overall time: 00:22:49 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 69675 / 12492174 = 0.0056 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 @ Fri, 26 Jun 2020 07:02:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1010109/SRX1010109.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1010109/SRX1010109.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1010109/SRX1010109.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1010109/SRX1010109.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 @ Fri, 26 Jun 2020 07:02:47: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:02:47: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:02:54: 1000000 INFO @ Fri, 26 Jun 2020 07:03:01: 2000000 INFO @ Fri, 26 Jun 2020 07:03:08: 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 @ Fri, 26 Jun 2020 07:03:15: 4000000 INFO @ Fri, 26 Jun 2020 07:03:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1010109/SRX1010109.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1010109/SRX1010109.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1010109/SRX1010109.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1010109/SRX1010109.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 @ Fri, 26 Jun 2020 07:03:17: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:03:17: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:03:23: 5000000 INFO @ Fri, 26 Jun 2020 07:03:24: 1000000 INFO @ Fri, 26 Jun 2020 07:03:32: 2000000 INFO @ Fri, 26 Jun 2020 07:03:33: 6000000 INFO @ Fri, 26 Jun 2020 07:03:40: 3000000 INFO @ Fri, 26 Jun 2020 07:03:43: 7000000 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 @ Fri, 26 Jun 2020 07:03:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1010109/SRX1010109.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1010109/SRX1010109.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1010109/SRX1010109.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1010109/SRX1010109.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 @ Fri, 26 Jun 2020 07:03:47: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:03:47: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:03:48: 4000000 INFO @ Fri, 26 Jun 2020 07:03:54: 8000000 INFO @ Fri, 26 Jun 2020 07:03:57: 5000000 INFO @ Fri, 26 Jun 2020 07:03:58: 1000000 INFO @ Fri, 26 Jun 2020 07:04:05: 9000000 INFO @ Fri, 26 Jun 2020 07:04:06: 6000000 INFO @ Fri, 26 Jun 2020 07:04:09: 2000000 INFO @ Fri, 26 Jun 2020 07:04:14: 7000000 INFO @ Fri, 26 Jun 2020 07:04:15: 10000000 INFO @ Fri, 26 Jun 2020 07:04:19: 3000000 INFO @ Fri, 26 Jun 2020 07:04:24: 8000000 INFO @ Fri, 26 Jun 2020 07:04:26: 11000000 INFO @ Fri, 26 Jun 2020 07:04:30: 4000000 INFO @ Fri, 26 Jun 2020 07:04:33: 9000000 INFO @ Fri, 26 Jun 2020 07:04:37: 12000000 INFO @ Fri, 26 Jun 2020 07:04:41: 5000000 INFO @ Fri, 26 Jun 2020 07:04:42: 10000000 INFO @ Fri, 26 Jun 2020 07:04:48: 13000000 INFO @ Fri, 26 Jun 2020 07:04:52: 11000000 INFO @ Fri, 26 Jun 2020 07:04:52: 6000000 INFO @ Fri, 26 Jun 2020 07:04:59: 14000000 INFO @ Fri, 26 Jun 2020 07:05:01: 12000000 INFO @ Fri, 26 Jun 2020 07:05:03: 7000000 INFO @ Fri, 26 Jun 2020 07:05:10: 15000000 INFO @ Fri, 26 Jun 2020 07:05:10: 13000000 INFO @ Fri, 26 Jun 2020 07:05:14: 8000000 INFO @ Fri, 26 Jun 2020 07:05:19: 14000000 INFO @ Fri, 26 Jun 2020 07:05:21: 16000000 INFO @ Fri, 26 Jun 2020 07:05:25: 9000000 INFO @ Fri, 26 Jun 2020 07:05:29: 15000000 INFO @ Fri, 26 Jun 2020 07:05:32: 17000000 INFO @ Fri, 26 Jun 2020 07:05:36: 10000000 INFO @ Fri, 26 Jun 2020 07:05:38: 16000000 INFO @ Fri, 26 Jun 2020 07:05:43: 18000000 INFO @ Fri, 26 Jun 2020 07:05:47: 11000000 INFO @ Fri, 26 Jun 2020 07:05:47: 17000000 INFO @ Fri, 26 Jun 2020 07:05:54: 19000000 INFO @ Fri, 26 Jun 2020 07:05:57: 18000000 INFO @ Fri, 26 Jun 2020 07:05:58: 12000000 INFO @ Fri, 26 Jun 2020 07:06:05: 20000000 INFO @ Fri, 26 Jun 2020 07:06:06: 19000000 INFO @ Fri, 26 Jun 2020 07:06:09: 13000000 INFO @ Fri, 26 Jun 2020 07:06:15: 20000000 INFO @ Fri, 26 Jun 2020 07:06:15: 21000000 INFO @ Fri, 26 Jun 2020 07:06:20: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:06:25: 21000000 INFO @ Fri, 26 Jun 2020 07:06:26: 22000000 INFO @ Fri, 26 Jun 2020 07:06:30: 15000000 INFO @ Fri, 26 Jun 2020 07:06:34: 22000000 INFO @ Fri, 26 Jun 2020 07:06:37: 23000000 INFO @ Fri, 26 Jun 2020 07:06:41: 16000000 INFO @ Fri, 26 Jun 2020 07:06:43: 23000000 INFO @ Fri, 26 Jun 2020 07:06:47: 24000000 INFO @ Fri, 26 Jun 2020 07:06:52: 17000000 INFO @ Fri, 26 Jun 2020 07:06:52: 24000000 INFO @ Fri, 26 Jun 2020 07:06:58: 25000000 INFO @ Fri, 26 Jun 2020 07:07:00: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 07:07:00: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 07:07:00: #1 total tags in treatment: 12399786 INFO @ Fri, 26 Jun 2020 07:07:00: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:07:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:07:00: #1 tags after filtering in treatment: 11542602 INFO @ Fri, 26 Jun 2020 07:07:00: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 07:07:00: #1 finished! INFO @ Fri, 26 Jun 2020 07:07:00: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:07:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:07:01: #2 number of paired peaks: 283 WARNING @ Fri, 26 Jun 2020 07:07:01: Fewer paired peaks (283) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 283 pairs to build model! INFO @ Fri, 26 Jun 2020 07:07:01: start model_add_line... INFO @ Fri, 26 Jun 2020 07:07:01: start X-correlation... INFO @ Fri, 26 Jun 2020 07:07:01: end of X-cor INFO @ Fri, 26 Jun 2020 07:07:01: #2 finished! INFO @ Fri, 26 Jun 2020 07:07:01: #2 predicted fragment length is 176 bps INFO @ Fri, 26 Jun 2020 07:07:01: #2 alternative fragment length(s) may be 176 bps INFO @ Fri, 26 Jun 2020 07:07:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1010109/SRX1010109.05_model.r INFO @ Fri, 26 Jun 2020 07:07:01: 25000000 INFO @ Fri, 26 Jun 2020 07:07:02: 18000000 INFO @ Fri, 26 Jun 2020 07:07:03: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 07:07:03: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 07:07:03: #1 total tags in treatment: 12399786 INFO @ Fri, 26 Jun 2020 07:07:03: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:07:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:07:03: #1 tags after filtering in treatment: 11542602 INFO @ Fri, 26 Jun 2020 07:07:03: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 07:07:03: #1 finished! INFO @ Fri, 26 Jun 2020 07:07:03: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:07:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:07:04: #2 number of paired peaks: 283 WARNING @ Fri, 26 Jun 2020 07:07:04: Fewer paired peaks (283) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 283 pairs to build model! INFO @ Fri, 26 Jun 2020 07:07:04: start model_add_line... INFO @ Fri, 26 Jun 2020 07:07:04: start X-correlation... INFO @ Fri, 26 Jun 2020 07:07:04: end of X-cor INFO @ Fri, 26 Jun 2020 07:07:04: #2 finished! INFO @ Fri, 26 Jun 2020 07:07:04: #2 predicted fragment length is 176 bps INFO @ Fri, 26 Jun 2020 07:07:04: #2 alternative fragment length(s) may be 176 bps INFO @ Fri, 26 Jun 2020 07:07:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1010109/SRX1010109.10_model.r INFO @ Fri, 26 Jun 2020 07:07:12: 19000000 INFO @ Fri, 26 Jun 2020 07:07:22: 20000000 INFO @ Fri, 26 Jun 2020 07:07:32: 21000000 INFO @ Fri, 26 Jun 2020 07:07:42: 22000000 WARNING @ Fri, 26 Jun 2020 07:07:49: #2 Since the d (176) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:07:49: #2 Since the d (176) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:07:49: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Fri, 26 Jun 2020 07:07:49: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Fri, 26 Jun 2020 07:07:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. WARNING @ Fri, 26 Jun 2020 07:07:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:07:49: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:07:49: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:07:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:07:49: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:07:52: 23000000 INFO @ Fri, 26 Jun 2020 07:08:02: 24000000 INFO @ Fri, 26 Jun 2020 07:08:11: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:08:11: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:08:12: 25000000 INFO @ Fri, 26 Jun 2020 07:08:13: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 07:08:13: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 07:08:13: #1 total tags in treatment: 12399786 INFO @ Fri, 26 Jun 2020 07:08:13: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:08:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:08:14: #1 tags after filtering in treatment: 11542602 INFO @ Fri, 26 Jun 2020 07:08:14: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 07:08:14: #1 finished! INFO @ Fri, 26 Jun 2020 07:08:14: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:08:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:08:14: #2 number of paired peaks: 283 WARNING @ Fri, 26 Jun 2020 07:08:14: Fewer paired peaks (283) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 283 pairs to build model! INFO @ Fri, 26 Jun 2020 07:08:14: start model_add_line... INFO @ Fri, 26 Jun 2020 07:08:14: start X-correlation... INFO @ Fri, 26 Jun 2020 07:08:14: end of X-cor INFO @ Fri, 26 Jun 2020 07:08:14: #2 finished! INFO @ Fri, 26 Jun 2020 07:08:14: #2 predicted fragment length is 176 bps INFO @ Fri, 26 Jun 2020 07:08:14: #2 alternative fragment length(s) may be 176 bps INFO @ Fri, 26 Jun 2020 07:08:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1010109/SRX1010109.20_model.r INFO @ Fri, 26 Jun 2020 07:08:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1010109/SRX1010109.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:08:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1010109/SRX1010109.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:08:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1010109/SRX1010109.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:08:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1010109/SRX1010109.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:09:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1010109/SRX1010109.05_summits.bed INFO @ Fri, 26 Jun 2020 07:09:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1010109/SRX1010109.10_summits.bed INFO @ Fri, 26 Jun 2020 07:09:00: Done! WARNING @ Fri, 26 Jun 2020 07:09:00: #2 Since the d (176) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:09:00: #2 You may need to consider one of the other alternative d(s): 176 WARNING @ Fri, 26 Jun 2020 07:09:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:09:00: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:09:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:09:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (273 records, 4 fields): 7 millis CompletedMACS2peakCalling pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (358 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:09:21: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:09:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1010109/SRX1010109.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:09:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1010109/SRX1010109.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:09:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1010109/SRX1010109.20_summits.bed INFO @ Fri, 26 Jun 2020 07:09:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (193 records, 4 fields): 2 millis CompletedMACS2peakCalling