Job ID = 6497575 SRX = SRX747301 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:14:59 prefetch.2.10.7: 1) Downloading 'SRR1634999'... 2020-06-25T22:14:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:16:43 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:16:44 prefetch.2.10.7: 'SRR1634999' is valid 2020-06-25T22:16:44 prefetch.2.10.7: 1) 'SRR1634999' was downloaded successfully 2020-06-25T22:17:17 prefetch.2.10.7: 'SRR1634999' has 6 unresolved dependencies 2020-06-25T22:17:17 prefetch.2.10.7: 2) Downloading 'ncbi-acc:BX284601.4?vdb-ctx=refseq'... 2020-06-25T22:17:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:17:32 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:17:32 prefetch.2.10.7: 2) 'ncbi-acc:BX284601.4?vdb-ctx=refseq' was downloaded successfully 2020-06-25T22:17:32 prefetch.2.10.7: 3) Downloading 'ncbi-acc:BX284602.4?vdb-ctx=refseq'... 2020-06-25T22:17:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:18:32 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:18:32 prefetch.2.10.7: 3) 'ncbi-acc:BX284602.4?vdb-ctx=refseq' was downloaded successfully 2020-06-25T22:18:32 prefetch.2.10.7: 4) Downloading 'ncbi-acc:BX284603.3?vdb-ctx=refseq'... 2020-06-25T22:18:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:18:48 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:18:48 prefetch.2.10.7: 4) 'ncbi-acc:BX284603.3?vdb-ctx=refseq' was downloaded successfully 2020-06-25T22:18:48 prefetch.2.10.7: 5) Downloading 'ncbi-acc:BX284604.3?vdb-ctx=refseq'... 2020-06-25T22:18:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:19:05 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:19:05 prefetch.2.10.7: 5) 'ncbi-acc:BX284604.3?vdb-ctx=refseq' was downloaded successfully 2020-06-25T22:19:05 prefetch.2.10.7: 6) Downloading 'ncbi-acc:BX284605.4?vdb-ctx=refseq'... 2020-06-25T22:19:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:19:23 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:19:23 prefetch.2.10.7: 6) 'ncbi-acc:BX284605.4?vdb-ctx=refseq' was downloaded successfully 2020-06-25T22:19:23 prefetch.2.10.7: 7) Downloading 'ncbi-acc:BX284606.4?vdb-ctx=refseq'... 2020-06-25T22:19:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:21:13 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:21:13 prefetch.2.10.7: 7) 'ncbi-acc:BX284606.4?vdb-ctx=refseq' was downloaded successfully Read 28914131 spots for SRR1634999/SRR1634999.sra Written 28914131 spots for SRR1634999/SRR1634999.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: 00:00:01 Multiseed full-index search: 00:03:30 28914131 reads; of these: 28914131 (100.00%) were unpaired; of these: 1264778 (4.37%) aligned 0 times 23594806 (81.60%) aligned exactly 1 time 4054547 (14.02%) aligned >1 times 95.63% overall alignment rate Time searching: 00:03:31 Overall time: 00:03:31 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] 5377468 / 27649353 = 0.1945 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 07:32:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX747301/SRX747301.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX747301/SRX747301.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX747301/SRX747301.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX747301/SRX747301.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 07:32:06: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:32:06: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:32:12: 1000000 INFO @ Fri, 26 Jun 2020 07:32:18: 2000000 INFO @ Fri, 26 Jun 2020 07:32:25: 3000000 INFO @ Fri, 26 Jun 2020 07:32:31: 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 @ Fri, 26 Jun 2020 07:32:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX747301/SRX747301.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX747301/SRX747301.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX747301/SRX747301.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX747301/SRX747301.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 07:32:36: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:32:36: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:32:38: 5000000 INFO @ Fri, 26 Jun 2020 07:32:42: 1000000 INFO @ Fri, 26 Jun 2020 07:32:45: 6000000 INFO @ Fri, 26 Jun 2020 07:32:49: 2000000 INFO @ Fri, 26 Jun 2020 07:32:51: 7000000 INFO @ Fri, 26 Jun 2020 07:32:55: 3000000 INFO @ Fri, 26 Jun 2020 07:32:58: 8000000 INFO @ Fri, 26 Jun 2020 07:33:01: 4000000 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 07:33:04: 9000000 INFO @ Fri, 26 Jun 2020 07:33:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX747301/SRX747301.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX747301/SRX747301.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX747301/SRX747301.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX747301/SRX747301.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 07:33:06: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:33:06: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:33:08: 5000000 INFO @ Fri, 26 Jun 2020 07:33:11: 10000000 INFO @ Fri, 26 Jun 2020 07:33:12: 1000000 INFO @ Fri, 26 Jun 2020 07:33:15: 6000000 INFO @ Fri, 26 Jun 2020 07:33:17: 11000000 INFO @ Fri, 26 Jun 2020 07:33:19: 2000000 INFO @ Fri, 26 Jun 2020 07:33:21: 7000000 INFO @ Fri, 26 Jun 2020 07:33:24: 12000000 INFO @ Fri, 26 Jun 2020 07:33:26: 3000000 INFO @ Fri, 26 Jun 2020 07:33:28: 8000000 INFO @ Fri, 26 Jun 2020 07:33:31: 13000000 INFO @ Fri, 26 Jun 2020 07:33:32: 4000000 INFO @ Fri, 26 Jun 2020 07:33:35: 9000000 INFO @ Fri, 26 Jun 2020 07:33:38: 14000000 INFO @ Fri, 26 Jun 2020 07:33:39: 5000000 INFO @ Fri, 26 Jun 2020 07:33:42: 10000000 INFO @ Fri, 26 Jun 2020 07:33:45: 15000000 INFO @ Fri, 26 Jun 2020 07:33:45: 6000000 INFO @ Fri, 26 Jun 2020 07:33:48: 11000000 INFO @ Fri, 26 Jun 2020 07:33:51: 16000000 INFO @ Fri, 26 Jun 2020 07:33:52: 7000000 INFO @ Fri, 26 Jun 2020 07:33:55: 12000000 INFO @ Fri, 26 Jun 2020 07:33:58: 17000000 INFO @ Fri, 26 Jun 2020 07:33:59: 8000000 INFO @ Fri, 26 Jun 2020 07:34:02: 13000000 INFO @ Fri, 26 Jun 2020 07:34:05: 18000000 INFO @ Fri, 26 Jun 2020 07:34:05: 9000000 INFO @ Fri, 26 Jun 2020 07:34:08: 14000000 INFO @ Fri, 26 Jun 2020 07:34:11: 19000000 INFO @ Fri, 26 Jun 2020 07:34:12: 10000000 INFO @ Fri, 26 Jun 2020 07:34:15: 15000000 INFO @ Fri, 26 Jun 2020 07:34:18: 20000000 INFO @ Fri, 26 Jun 2020 07:34:18: 11000000 INFO @ Fri, 26 Jun 2020 07:34:21: 16000000 INFO @ Fri, 26 Jun 2020 07:34:24: 21000000 INFO @ Fri, 26 Jun 2020 07:34:25: 12000000 INFO @ Fri, 26 Jun 2020 07:34:28: 17000000 INFO @ Fri, 26 Jun 2020 07:34:31: 22000000 INFO @ Fri, 26 Jun 2020 07:34:32: 13000000 INFO @ Fri, 26 Jun 2020 07:34:33: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:34:33: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:34:33: #1 total tags in treatment: 22271885 INFO @ Fri, 26 Jun 2020 07:34:33: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:34:33: #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 07:34:33: #1 tags after filtering in treatment: 22271885 INFO @ Fri, 26 Jun 2020 07:34:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:34:33: #1 finished! INFO @ Fri, 26 Jun 2020 07:34:33: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:34:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:34:35: #2 number of paired peaks: 169 WARNING @ Fri, 26 Jun 2020 07:34:35: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Fri, 26 Jun 2020 07:34:35: start model_add_line... INFO @ Fri, 26 Jun 2020 07:34:35: start X-correlation... INFO @ Fri, 26 Jun 2020 07:34:35: end of X-cor INFO @ Fri, 26 Jun 2020 07:34:35: #2 finished! INFO @ Fri, 26 Jun 2020 07:34:35: #2 predicted fragment length is 101 bps INFO @ Fri, 26 Jun 2020 07:34:35: #2 alternative fragment length(s) may be 3,101 bps INFO @ Fri, 26 Jun 2020 07:34:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX747301/SRX747301.05_model.r INFO @ Fri, 26 Jun 2020 07:34:35: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:34:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:34:35: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:34:38: 14000000 INFO @ Fri, 26 Jun 2020 07:34:41: 19000000 INFO @ Fri, 26 Jun 2020 07:34:45: 15000000 INFO @ Fri, 26 Jun 2020 07:34:48: 20000000 INFO @ Fri, 26 Jun 2020 07:34:51: 16000000 INFO @ Fri, 26 Jun 2020 07:34:54: 21000000 INFO @ Fri, 26 Jun 2020 07:34:58: 17000000 INFO @ Fri, 26 Jun 2020 07:35:01: 22000000 INFO @ Fri, 26 Jun 2020 07:35:02: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:35:02: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:35:02: #1 total tags in treatment: 22271885 INFO @ Fri, 26 Jun 2020 07:35:02: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:35:02: #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 07:35:03: #1 tags after filtering in treatment: 22271885 INFO @ Fri, 26 Jun 2020 07:35:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:35:03: #1 finished! INFO @ Fri, 26 Jun 2020 07:35:03: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:35:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:35:04: 18000000 INFO @ Fri, 26 Jun 2020 07:35:04: #2 number of paired peaks: 169 WARNING @ Fri, 26 Jun 2020 07:35:04: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Fri, 26 Jun 2020 07:35:04: start model_add_line... INFO @ Fri, 26 Jun 2020 07:35:04: start X-correlation... INFO @ Fri, 26 Jun 2020 07:35:04: end of X-cor INFO @ Fri, 26 Jun 2020 07:35:04: #2 finished! INFO @ Fri, 26 Jun 2020 07:35:04: #2 predicted fragment length is 101 bps INFO @ Fri, 26 Jun 2020 07:35:04: #2 alternative fragment length(s) may be 3,101 bps INFO @ Fri, 26 Jun 2020 07:35:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX747301/SRX747301.10_model.r INFO @ Fri, 26 Jun 2020 07:35:04: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:35:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:35:10: 19000000 INFO @ Fri, 26 Jun 2020 07:35:16: 20000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:35:22: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:35:22: 21000000 INFO @ Fri, 26 Jun 2020 07:35:28: 22000000 INFO @ Fri, 26 Jun 2020 07:35:30: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:35:30: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:35:30: #1 total tags in treatment: 22271885 INFO @ Fri, 26 Jun 2020 07:35:30: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:35:30: #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 07:35:30: #1 tags after filtering in treatment: 22271885 INFO @ Fri, 26 Jun 2020 07:35:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:35:30: #1 finished! INFO @ Fri, 26 Jun 2020 07:35:30: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:35:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:35:32: #2 number of paired peaks: 169 WARNING @ Fri, 26 Jun 2020 07:35:32: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Fri, 26 Jun 2020 07:35:32: start model_add_line... INFO @ Fri, 26 Jun 2020 07:35:32: start X-correlation... INFO @ Fri, 26 Jun 2020 07:35:32: end of X-cor INFO @ Fri, 26 Jun 2020 07:35:32: #2 finished! INFO @ Fri, 26 Jun 2020 07:35:32: #2 predicted fragment length is 101 bps INFO @ Fri, 26 Jun 2020 07:35:32: #2 alternative fragment length(s) may be 3,101 bps INFO @ Fri, 26 Jun 2020 07:35:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX747301/SRX747301.20_model.r INFO @ Fri, 26 Jun 2020 07:35:32: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:35:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:35:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX747301/SRX747301.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:35:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX747301/SRX747301.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:35:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX747301/SRX747301.05_summits.bed INFO @ Fri, 26 Jun 2020 07:35:46: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (18754 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:35:48: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:36:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX747301/SRX747301.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:36:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX747301/SRX747301.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:36:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX747301/SRX747301.10_summits.bed INFO @ Fri, 26 Jun 2020 07:36:11: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (9232 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:36:17: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:36:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX747301/SRX747301.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:36:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX747301/SRX747301.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:36:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX747301/SRX747301.20_summits.bed INFO @ Fri, 26 Jun 2020 07:36:40: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (3111 records, 4 fields): 5 millis CompletedMACS2peakCalling