Job ID = 5790639 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-21T19:40:06 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-21T19:40:06 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 50,289,180 reads read : 100,578,360 reads written : 50,289,180 reads 0-length : 50,289,180 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:04 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:33:06 50289180 reads; of these: 50289180 (100.00%) were unpaired; of these: 5815848 (11.56%) aligned 0 times 41015551 (81.56%) aligned exactly 1 time 3457781 (6.88%) aligned >1 times 88.44% overall alignment rate Time searching: 00:33:12 Overall time: 00:33:12 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 20 files... [bam_rmdupse_core] 26015464 / 44473332 = 0.5850 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 @ Wed, 22 Apr 2020 05:49:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299283/SRX5299283.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299283/SRX5299283.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299283/SRX5299283.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299283/SRX5299283.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Apr 2020 05:49:57: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:49:57: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:50:05: 1000000 INFO @ Wed, 22 Apr 2020 05:50:14: 2000000 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 @ Wed, 22 Apr 2020 05:50:22: 3000000 INFO @ Wed, 22 Apr 2020 05:50:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299283/SRX5299283.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299283/SRX5299283.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299283/SRX5299283.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299283/SRX5299283.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Apr 2020 05:50:27: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:50:27: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:50:31: 4000000 INFO @ Wed, 22 Apr 2020 05:50:36: 1000000 INFO @ Wed, 22 Apr 2020 05:50:41: 5000000 INFO @ Wed, 22 Apr 2020 05:50:44: 2000000 INFO @ Wed, 22 Apr 2020 05:50:50: 6000000 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 @ Wed, 22 Apr 2020 05:50:53: 3000000 INFO @ Wed, 22 Apr 2020 05:50:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5299283/SRX5299283.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5299283/SRX5299283.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5299283/SRX5299283.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5299283/SRX5299283.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Apr 2020 05:50:57: #1 read tag files... INFO @ Wed, 22 Apr 2020 05:50:57: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 05:51:00: 7000000 INFO @ Wed, 22 Apr 2020 05:51:02: 4000000 INFO @ Wed, 22 Apr 2020 05:51:05: 1000000 INFO @ Wed, 22 Apr 2020 05:51:10: 8000000 INFO @ Wed, 22 Apr 2020 05:51:10: 5000000 INFO @ Wed, 22 Apr 2020 05:51:14: 2000000 INFO @ Wed, 22 Apr 2020 05:51:19: 6000000 INFO @ Wed, 22 Apr 2020 05:51:20: 9000000 INFO @ Wed, 22 Apr 2020 05:51:23: 3000000 INFO @ Wed, 22 Apr 2020 05:51:27: 7000000 INFO @ Wed, 22 Apr 2020 05:51:29: 10000000 INFO @ Wed, 22 Apr 2020 05:51:31: 4000000 INFO @ Wed, 22 Apr 2020 05:51:36: 8000000 INFO @ Wed, 22 Apr 2020 05:51:39: 11000000 INFO @ Wed, 22 Apr 2020 05:51:40: 5000000 INFO @ Wed, 22 Apr 2020 05:51:45: 9000000 INFO @ Wed, 22 Apr 2020 05:51:48: 12000000 INFO @ Wed, 22 Apr 2020 05:51:49: 6000000 INFO @ Wed, 22 Apr 2020 05:51:53: 10000000 INFO @ Wed, 22 Apr 2020 05:51:57: 7000000 INFO @ Wed, 22 Apr 2020 05:51:58: 13000000 INFO @ Wed, 22 Apr 2020 05:52:02: 11000000 INFO @ Wed, 22 Apr 2020 05:52:06: 8000000 INFO @ Wed, 22 Apr 2020 05:52:07: 14000000 INFO @ Wed, 22 Apr 2020 05:52:11: 12000000 INFO @ Wed, 22 Apr 2020 05:52:14: 9000000 INFO @ Wed, 22 Apr 2020 05:52:17: 15000000 INFO @ Wed, 22 Apr 2020 05:52:19: 13000000 INFO @ Wed, 22 Apr 2020 05:52:23: 10000000 INFO @ Wed, 22 Apr 2020 05:52:26: 16000000 INFO @ Wed, 22 Apr 2020 05:52:28: 14000000 INFO @ Wed, 22 Apr 2020 05:52:32: 11000000 INFO @ Wed, 22 Apr 2020 05:52:36: 17000000 INFO @ Wed, 22 Apr 2020 05:52:36: 15000000 INFO @ Wed, 22 Apr 2020 05:52:40: 12000000 INFO @ Wed, 22 Apr 2020 05:52:45: 18000000 INFO @ Wed, 22 Apr 2020 05:52:45: 16000000 INFO @ Wed, 22 Apr 2020 05:52:49: 13000000 INFO @ Wed, 22 Apr 2020 05:52:49: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 05:52:49: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 05:52:49: #1 total tags in treatment: 18457868 INFO @ Wed, 22 Apr 2020 05:52:49: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:52:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 05:52:50: #1 tags after filtering in treatment: 18457573 INFO @ Wed, 22 Apr 2020 05:52:50: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:52:50: #1 finished! INFO @ Wed, 22 Apr 2020 05:52:50: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:52:50: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:52:51: #2 number of paired peaks: 17090 INFO @ Wed, 22 Apr 2020 05:52:51: start model_add_line... INFO @ Wed, 22 Apr 2020 05:52:52: start X-correlation... INFO @ Wed, 22 Apr 2020 05:52:52: end of X-cor INFO @ Wed, 22 Apr 2020 05:52:52: #2 finished! INFO @ Wed, 22 Apr 2020 05:52:52: #2 predicted fragment length is 177 bps INFO @ Wed, 22 Apr 2020 05:52:52: #2 alternative fragment length(s) may be 177 bps INFO @ Wed, 22 Apr 2020 05:52:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299283/SRX5299283.05_model.r WARNING @ Wed, 22 Apr 2020 05:52:52: #2 Since the d (177) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 05:52:52: #2 You may need to consider one of the other alternative d(s): 177 WARNING @ Wed, 22 Apr 2020 05:52:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 05:52:52: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:52:52: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:52:54: 17000000 INFO @ Wed, 22 Apr 2020 05:52:57: 14000000 INFO @ Wed, 22 Apr 2020 05:53:03: 18000000 INFO @ Wed, 22 Apr 2020 05:53:06: 15000000 INFO @ Wed, 22 Apr 2020 05:53:07: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 05:53:07: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 05:53:07: #1 total tags in treatment: 18457868 INFO @ Wed, 22 Apr 2020 05:53:07: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:53:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 05:53:07: #1 tags after filtering in treatment: 18457573 INFO @ Wed, 22 Apr 2020 05:53:07: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:53:07: #1 finished! INFO @ Wed, 22 Apr 2020 05:53:07: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:53:07: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 05:53:09: #2 number of paired peaks: 17090 INFO @ Wed, 22 Apr 2020 05:53:09: start model_add_line... INFO @ Wed, 22 Apr 2020 05:53:09: start X-correlation... INFO @ Wed, 22 Apr 2020 05:53:09: end of X-cor INFO @ Wed, 22 Apr 2020 05:53:09: #2 finished! INFO @ Wed, 22 Apr 2020 05:53:09: #2 predicted fragment length is 177 bps INFO @ Wed, 22 Apr 2020 05:53:09: #2 alternative fragment length(s) may be 177 bps INFO @ Wed, 22 Apr 2020 05:53:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299283/SRX5299283.10_model.r WARNING @ Wed, 22 Apr 2020 05:53:09: #2 Since the d (177) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 05:53:09: #2 You may need to consider one of the other alternative d(s): 177 WARNING @ Wed, 22 Apr 2020 05:53:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 05:53:09: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:53:09: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:53:14: 16000000 INFO @ Wed, 22 Apr 2020 05:53:21: 17000000 INFO @ Wed, 22 Apr 2020 05:53:28: 18000000 INFO @ Wed, 22 Apr 2020 05:53:29: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 05:53:31: #1 tag size is determined as 102 bps INFO @ Wed, 22 Apr 2020 05:53:31: #1 tag size = 102 INFO @ Wed, 22 Apr 2020 05:53:31: #1 total tags in treatment: 18457868 INFO @ Wed, 22 Apr 2020 05:53:31: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 05:53:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 05:53:31: #1 tags after filtering in treatment: 18457573 INFO @ Wed, 22 Apr 2020 05:53:31: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 05:53:31: #1 finished! INFO @ Wed, 22 Apr 2020 05:53:31: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 05:53:31: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 05:53:33: #2 number of paired peaks: 17090 INFO @ Wed, 22 Apr 2020 05:53:33: start model_add_line... INFO @ Wed, 22 Apr 2020 05:53:33: start X-correlation... INFO @ Wed, 22 Apr 2020 05:53:33: end of X-cor INFO @ Wed, 22 Apr 2020 05:53:33: #2 finished! INFO @ Wed, 22 Apr 2020 05:53:33: #2 predicted fragment length is 177 bps INFO @ Wed, 22 Apr 2020 05:53:33: #2 alternative fragment length(s) may be 177 bps INFO @ Wed, 22 Apr 2020 05:53:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5299283/SRX5299283.20_model.r WARNING @ Wed, 22 Apr 2020 05:53:33: #2 Since the d (177) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 05:53:33: #2 You may need to consider one of the other alternative d(s): 177 WARNING @ Wed, 22 Apr 2020 05:53:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 05:53:33: #3 Call peaks... INFO @ Wed, 22 Apr 2020 05:53:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 05:53:47: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299283/SRX5299283.05_peaks.xls INFO @ Wed, 22 Apr 2020 05:53:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299283/SRX5299283.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:53:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299283/SRX5299283.05_summits.bed INFO @ Wed, 22 Apr 2020 05:53:47: Done! INFO @ Wed, 22 Apr 2020 05:53:48: #3 Call peaks for each chromosome... pass1 - making usageList (120 chroms): 5 millis pass2 - checking and writing primary data (22921 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 05:54:06: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299283/SRX5299283.10_peaks.xls INFO @ Wed, 22 Apr 2020 05:54:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299283/SRX5299283.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:54:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299283/SRX5299283.10_summits.bed INFO @ Wed, 22 Apr 2020 05:54:06: Done! INFO @ Wed, 22 Apr 2020 05:54:11: #3 Call peaks for each chromosome... pass1 - making usageList (115 chroms): 4 millis pass2 - checking and writing primary data (20981 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 05:54:29: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5299283/SRX5299283.20_peaks.xls INFO @ Wed, 22 Apr 2020 05:54:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5299283/SRX5299283.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 05:54:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5299283/SRX5299283.20_summits.bed INFO @ Wed, 22 Apr 2020 05:54:29: Done! pass1 - making usageList (108 chroms): 3 millis pass2 - checking and writing primary data (19189 records, 4 fields): 20 millis CompletedMACS2peakCalling