[2023-03-17 10:10:44,460] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:10:44,461] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:10:44,461] [INFO] DQC Reference Directory: /var/lib/cwl/stg617a9f81-80d9-46f6-b17a-381449135232/dqc_reference
[2023-03-17 10:10:45,552] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:10:45,553] [INFO] Task started: Prodigal
[2023-03-17 10:10:45,553] [INFO] Running command: cat /var/lib/cwl/stg969d58e4-fbb0-49da-81d5-f56846bf59b0/OceanDNA-b34630.fa | prodigal -d OceanDNA-b34630/cds.fna -a OceanDNA-b34630/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:11:07,539] [INFO] Task succeeded: Prodigal
[2023-03-17 10:11:07,539] [INFO] Task started: HMMsearch
[2023-03-17 10:11:07,539] [INFO] Running command: hmmsearch --tblout OceanDNA-b34630/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg617a9f81-80d9-46f6-b17a-381449135232/dqc_reference/reference_markers.hmm OceanDNA-b34630/protein.faa > /dev/null
[2023-03-17 10:11:07,761] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:11:07,761] [INFO] Found 6/6 markers.
[2023-03-17 10:11:07,783] [INFO] Query marker FASTA was written to OceanDNA-b34630/markers.fasta
[2023-03-17 10:11:07,785] [INFO] Task started: Blastn
[2023-03-17 10:11:07,785] [INFO] Running command: blastn -query OceanDNA-b34630/markers.fasta -db /var/lib/cwl/stg617a9f81-80d9-46f6-b17a-381449135232/dqc_reference/reference_markers.fasta -out OceanDNA-b34630/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:11:08,438] [INFO] Task succeeded: Blastn
[2023-03-17 10:11:08,439] [INFO] Selected 12 target genomes.
[2023-03-17 10:11:08,440] [INFO] Target genome list was writen to OceanDNA-b34630/target_genomes.txt
[2023-03-17 10:11:08,490] [INFO] Task started: fastANI
[2023-03-17 10:11:08,490] [INFO] Running command: fastANI --query /var/lib/cwl/stg969d58e4-fbb0-49da-81d5-f56846bf59b0/OceanDNA-b34630.fa --refList OceanDNA-b34630/target_genomes.txt --output OceanDNA-b34630/fastani_result.tsv --threads 1
[2023-03-17 10:11:18,268] [INFO] Task succeeded: fastANI
[2023-03-17 10:11:18,268] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg617a9f81-80d9-46f6-b17a-381449135232/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:11:18,269] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg617a9f81-80d9-46f6-b17a-381449135232/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:11:18,276] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:11:18,276] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 10:11:18,276] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Arsukibacterium indicum	strain=SM2107	GCA_019100565.1	2848612	2848612	type	True	82.1562	887	1275	95	below_threshold
Arsukibacterium perlucidum	strain=DSM 18276	GCA_000382165.1	368811	368811	type	True	81.8625	820	1275	95	below_threshold
Arsukibacterium tuosuense	strain=CGMCC 1.12461	GCA_900215315.1	1323745	1323745	type	True	81.6356	871	1275	95	below_threshold
Rheinheimera lutimaris	strain=YQF-2	GCA_013283795.1	2740584	2740584	type	True	78.6583	380	1275	95	below_threshold
Rheinheimera pleomorphica	strain=PKS7	GCA_011634895.1	2703963	2703963	type	True	78.6382	374	1275	95	below_threshold
Rheinheimera pacifica	strain=DSM 17616	GCA_900108485.1	173990	173990	type	True	78.4792	410	1275	95	below_threshold
Rheinheimera baltica	strain=DSM 14885	GCA_000425345.1	67576	67576	type	True	78.2045	290	1275	95	below_threshold
Rheinheimera hassiensis	strain=LMG 27268	GCA_022436675.1	1193627	1193627	type	True	78.2003	390	1275	95	below_threshold
Alishewanella aestuarii	strain=B11	GCA_000280055.1	453835	453835	type	True	78.1089	279	1275	95	below_threshold
Rheinheimera riviphila	strain=KYPC3	GCA_004005945.1	1834037	1834037	type	True	77.0065	179	1275	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 10:11:18,277] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34630/tc_result.tsv
[2023-03-17 10:11:18,277] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:11:18,277] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:11:18,277] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg617a9f81-80d9-46f6-b17a-381449135232/dqc_reference/checkm_data
[2023-03-17 10:11:18,277] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:11:18,282] [INFO] Task started: CheckM
[2023-03-17 10:11:18,283] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34630/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34630/checkm_input OceanDNA-b34630/checkm_result
[2023-03-17 10:12:12,983] [INFO] Task succeeded: CheckM
[2023-03-17 10:12:12,984] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 10:12:13,007] [INFO] ===== Completeness check finished =====
[2023-03-17 10:12:13,007] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:12:13,008] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34630/markers.fasta)
[2023-03-17 10:12:13,009] [INFO] Task started: Blastn
[2023-03-17 10:12:13,009] [INFO] Running command: blastn -query OceanDNA-b34630/markers.fasta -db /var/lib/cwl/stg617a9f81-80d9-46f6-b17a-381449135232/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34630/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:12:14,059] [INFO] Task succeeded: Blastn
[2023-03-17 10:12:14,060] [INFO] Selected 7 target genomes.
[2023-03-17 10:12:14,060] [INFO] Target genome list was writen to OceanDNA-b34630/target_genomes_gtdb.txt
[2023-03-17 10:12:14,098] [INFO] Task started: fastANI
[2023-03-17 10:12:14,098] [INFO] Running command: fastANI --query /var/lib/cwl/stg969d58e4-fbb0-49da-81d5-f56846bf59b0/OceanDNA-b34630.fa --refList OceanDNA-b34630/target_genomes_gtdb.txt --output OceanDNA-b34630/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:12:20,502] [INFO] Task succeeded: fastANI
[2023-03-17 10:12:20,507] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 10:12:20,507] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_002415085.1	s__Arsukibacterium sp002415085	99.9916	1261	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	99.96	99.86	0.96	0.90	7	conclusive
GCA_002364615.1	s__Arsukibacterium sp002364615	85.9887	1038	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	99.93	99.93	0.99	0.99	2	-
GCF_019100565.1	s__Arsukibacterium sp019100565	82.15	887	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382165.1	s__Arsukibacterium perlucidum	81.8452	821	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402695.1	s__Arsukibacterium sp018402695	81.7179	859	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215315.1	s__Arsukibacterium tuosuense	81.6427	870	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000987775.1	s__Arsukibacterium ikkense	80.803	762	1275	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Arsukibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 10:12:20,507] [INFO] GTDB search result was written to OceanDNA-b34630/result_gtdb.tsv
[2023-03-17 10:12:20,507] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:12:20,508] [INFO] DFAST_QC result json was written to OceanDNA-b34630/dqc_result.json
[2023-03-17 10:12:20,508] [INFO] DFAST_QC completed!
[2023-03-17 10:12:20,508] [INFO] Total running time: 0h1m36s