Job ID = 6367906 SRX = SRX4194199 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:38:59 prefetch.2.10.7: 1) Downloading 'SRR7291483'... 2020-06-15T23:38:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:40:58 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:40:58 prefetch.2.10.7: 'SRR7291483' is valid 2020-06-15T23:40:58 prefetch.2.10.7: 1) 'SRR7291483' was downloaded successfully 2020-06-15T23:40:58 prefetch.2.10.7: 'SRR7291483' has 0 unresolved dependencies Read 6916715 spots for SRR7291483/SRR7291483.sra Written 6916715 spots for SRR7291483/SRR7291483.sra 2020-06-15T23:41:36 prefetch.2.10.7: 1) Downloading 'SRR7291484'... 2020-06-15T23:41:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:42:29 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:42:29 prefetch.2.10.7: 'SRR7291484' is valid 2020-06-15T23:42:29 prefetch.2.10.7: 1) 'SRR7291484' was downloaded successfully 2020-06-15T23:42:29 prefetch.2.10.7: 'SRR7291484' has 0 unresolved dependencies Read 6787209 spots for SRR7291484/SRR7291484.sra Written 6787209 spots for SRR7291484/SRR7291484.sra 2020-06-15T23:43:04 prefetch.2.10.7: 1) Downloading 'SRR7291485'... 2020-06-15T23:43:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:44:35 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:44:36 prefetch.2.10.7: 'SRR7291485' is valid 2020-06-15T23:44:36 prefetch.2.10.7: 1) 'SRR7291485' was downloaded successfully 2020-06-15T23:44:36 prefetch.2.10.7: 'SRR7291485' has 0 unresolved dependencies Read 6916548 spots for SRR7291485/SRR7291485.sra Written 6916548 spots for SRR7291485/SRR7291485.sra 2020-06-15T23:45:10 prefetch.2.10.7: 1) Downloading 'SRR7291486'... 2020-06-15T23:45:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:47:10 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:47:10 prefetch.2.10.7: 'SRR7291486' is valid 2020-06-15T23:47:10 prefetch.2.10.7: 1) 'SRR7291486' was downloaded successfully 2020-06-15T23:47:10 prefetch.2.10.7: 'SRR7291486' has 0 unresolved dependencies Read 6701121 spots for SRR7291486/SRR7291486.sra Written 6701121 spots for SRR7291486/SRR7291486.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: 00:09:54 27321593 reads; of these: 27321593 (100.00%) were unpaired; of these: 1033493 (3.78%) aligned 0 times 21414107 (78.38%) aligned exactly 1 time 4873993 (17.84%) aligned >1 times 96.22% overall alignment rate Time searching: 00:09:54 Overall time: 00:09:54 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] 6817379 / 26288100 = 0.2593 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 09:05:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194199/SRX4194199.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194199/SRX4194199.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194199/SRX4194199.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194199/SRX4194199.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 09:05:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:05:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:05:37: 1000000 INFO @ Tue, 16 Jun 2020 09:05:43: 2000000 INFO @ Tue, 16 Jun 2020 09:05:50: 3000000 INFO @ Tue, 16 Jun 2020 09:05:57: 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 09:06:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194199/SRX4194199.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194199/SRX4194199.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194199/SRX4194199.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194199/SRX4194199.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 09:06:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:06:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:06:04: 5000000 INFO @ Tue, 16 Jun 2020 09:06:09: 1000000 INFO @ Tue, 16 Jun 2020 09:06:13: 6000000 INFO @ Tue, 16 Jun 2020 09:06:17: 2000000 INFO @ Tue, 16 Jun 2020 09:06:21: 7000000 INFO @ Tue, 16 Jun 2020 09:06:26: 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 09:06:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194199/SRX4194199.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194199/SRX4194199.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194199/SRX4194199.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194199/SRX4194199.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 09:06:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:06:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:06:30: 8000000 INFO @ Tue, 16 Jun 2020 09:06:35: 4000000 INFO @ Tue, 16 Jun 2020 09:06:38: 1000000 INFO @ Tue, 16 Jun 2020 09:06:39: 9000000 INFO @ Tue, 16 Jun 2020 09:06:44: 5000000 INFO @ Tue, 16 Jun 2020 09:06:47: 2000000 INFO @ Tue, 16 Jun 2020 09:06:47: 10000000 INFO @ Tue, 16 Jun 2020 09:06:54: 6000000 INFO @ Tue, 16 Jun 2020 09:06:55: 3000000 INFO @ Tue, 16 Jun 2020 09:06:56: 11000000 INFO @ Tue, 16 Jun 2020 09:07:03: 7000000 INFO @ Tue, 16 Jun 2020 09:07:04: 4000000 INFO @ Tue, 16 Jun 2020 09:07:04: 12000000 INFO @ Tue, 16 Jun 2020 09:07:12: 8000000 INFO @ Tue, 16 Jun 2020 09:07:13: 5000000 INFO @ Tue, 16 Jun 2020 09:07:13: 13000000 INFO @ Tue, 16 Jun 2020 09:07:21: 9000000 INFO @ Tue, 16 Jun 2020 09:07:22: 6000000 INFO @ Tue, 16 Jun 2020 09:07:23: 14000000 INFO @ Tue, 16 Jun 2020 09:07:30: 10000000 INFO @ Tue, 16 Jun 2020 09:07:31: 7000000 INFO @ Tue, 16 Jun 2020 09:07:32: 15000000 INFO @ Tue, 16 Jun 2020 09:07:39: 11000000 INFO @ Tue, 16 Jun 2020 09:07:40: 8000000 INFO @ Tue, 16 Jun 2020 09:07:43: 16000000 INFO @ Tue, 16 Jun 2020 09:07:48: 12000000 INFO @ Tue, 16 Jun 2020 09:07:49: 9000000 INFO @ Tue, 16 Jun 2020 09:07:52: 17000000 INFO @ Tue, 16 Jun 2020 09:07:57: 13000000 INFO @ Tue, 16 Jun 2020 09:07:58: 10000000 INFO @ Tue, 16 Jun 2020 09:08:02: 18000000 INFO @ Tue, 16 Jun 2020 09:08:07: 11000000 INFO @ Tue, 16 Jun 2020 09:08:07: 14000000 INFO @ Tue, 16 Jun 2020 09:08:11: 19000000 INFO @ Tue, 16 Jun 2020 09:08:15: #1 tag size is determined as 70 bps INFO @ Tue, 16 Jun 2020 09:08:15: #1 tag size = 70 INFO @ Tue, 16 Jun 2020 09:08:15: #1 total tags in treatment: 19470721 INFO @ Tue, 16 Jun 2020 09:08:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:08:15: #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 09:08:16: #1 tags after filtering in treatment: 19470721 INFO @ Tue, 16 Jun 2020 09:08:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:08:16: #1 finished! INFO @ Tue, 16 Jun 2020 09:08:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:08:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:08:16: 12000000 INFO @ Tue, 16 Jun 2020 09:08:16: 15000000 INFO @ Tue, 16 Jun 2020 09:08:17: #2 number of paired peaks: 351 WARNING @ Tue, 16 Jun 2020 09:08:17: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Tue, 16 Jun 2020 09:08:17: start model_add_line... INFO @ Tue, 16 Jun 2020 09:08:17: start X-correlation... INFO @ Tue, 16 Jun 2020 09:08:17: end of X-cor INFO @ Tue, 16 Jun 2020 09:08:17: #2 finished! INFO @ Tue, 16 Jun 2020 09:08:17: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 09:08:17: #2 alternative fragment length(s) may be 2,45 bps INFO @ Tue, 16 Jun 2020 09:08:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194199/SRX4194199.05_model.r WARNING @ Tue, 16 Jun 2020 09:08:17: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:08:17: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Tue, 16 Jun 2020 09:08:17: #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 09:08:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:08:17: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:08:25: 13000000 INFO @ Tue, 16 Jun 2020 09:08:27: 16000000 INFO @ Tue, 16 Jun 2020 09:08:33: 14000000 INFO @ Tue, 16 Jun 2020 09:08:37: 17000000 INFO @ Tue, 16 Jun 2020 09:08:42: 15000000 INFO @ Tue, 16 Jun 2020 09:08:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:08:47: 18000000 INFO @ Tue, 16 Jun 2020 09:08:50: 16000000 INFO @ Tue, 16 Jun 2020 09:08:58: 19000000 INFO @ Tue, 16 Jun 2020 09:08:59: 17000000 INFO @ Tue, 16 Jun 2020 09:09:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194199/SRX4194199.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:09:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194199/SRX4194199.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:09:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194199/SRX4194199.05_summits.bed INFO @ Tue, 16 Jun 2020 09:09:02: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:09:03: #1 tag size is determined as 70 bps INFO @ Tue, 16 Jun 2020 09:09:03: #1 tag size = 70 INFO @ Tue, 16 Jun 2020 09:09:03: #1 total tags in treatment: 19470721 INFO @ Tue, 16 Jun 2020 09:09:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:09:03: #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 09:09:03: #1 tags after filtering in treatment: 19470721 INFO @ Tue, 16 Jun 2020 09:09:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:09:03: #1 finished! INFO @ Tue, 16 Jun 2020 09:09:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:09:03: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:09:04: #2 number of paired peaks: 351 WARNING @ Tue, 16 Jun 2020 09:09:04: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Tue, 16 Jun 2020 09:09:04: start model_add_line... INFO @ Tue, 16 Jun 2020 09:09:04: start X-correlation... INFO @ Tue, 16 Jun 2020 09:09:04: end of X-cor INFO @ Tue, 16 Jun 2020 09:09:04: #2 finished! INFO @ Tue, 16 Jun 2020 09:09:04: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 09:09:04: #2 alternative fragment length(s) may be 2,45 bps INFO @ Tue, 16 Jun 2020 09:09:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194199/SRX4194199.10_model.r WARNING @ Tue, 16 Jun 2020 09:09:04: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:09:04: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Tue, 16 Jun 2020 09:09:04: #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 09:09:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:09:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:09:07: 18000000 INFO @ Tue, 16 Jun 2020 09:09:15: 19000000 INFO @ Tue, 16 Jun 2020 09:09:18: #1 tag size is determined as 70 bps INFO @ Tue, 16 Jun 2020 09:09:18: #1 tag size = 70 INFO @ Tue, 16 Jun 2020 09:09:18: #1 total tags in treatment: 19470721 INFO @ Tue, 16 Jun 2020 09:09:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:09:18: #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 09:09:18: #1 tags after filtering in treatment: 19470721 INFO @ Tue, 16 Jun 2020 09:09:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:09:18: #1 finished! INFO @ Tue, 16 Jun 2020 09:09:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:09:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:09:20: #2 number of paired peaks: 351 WARNING @ Tue, 16 Jun 2020 09:09:20: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Tue, 16 Jun 2020 09:09:20: start model_add_line... INFO @ Tue, 16 Jun 2020 09:09:20: start X-correlation... INFO @ Tue, 16 Jun 2020 09:09:20: end of X-cor INFO @ Tue, 16 Jun 2020 09:09:20: #2 finished! INFO @ Tue, 16 Jun 2020 09:09:20: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 09:09:20: #2 alternative fragment length(s) may be 2,45 bps INFO @ Tue, 16 Jun 2020 09:09:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194199/SRX4194199.20_model.r WARNING @ Tue, 16 Jun 2020 09:09:20: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:09:20: #2 You may need to consider one of the other alternative d(s): 2,45 WARNING @ Tue, 16 Jun 2020 09:09:20: #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 09:09:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:09:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:09:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:09:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194199/SRX4194199.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:09:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194199/SRX4194199.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:09:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194199/SRX4194199.10_summits.bed INFO @ Tue, 16 Jun 2020 09:09:50: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:09:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:10:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194199/SRX4194199.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:10:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194199/SRX4194199.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:10:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194199/SRX4194199.20_summits.bed INFO @ Tue, 16 Jun 2020 09:10:06: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling