[2024-01-25 20:04:20,693] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:04:20,695] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:04:20,695] [INFO] DQC Reference Directory: /var/lib/cwl/stgea0e732a-8b49-4cf1-97fd-8c0f41ccf914/dqc_reference
[2024-01-25 20:04:21,929] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:04:21,930] [INFO] Task started: Prodigal
[2024-01-25 20:04:21,930] [INFO] Running command: gunzip -c /var/lib/cwl/stg44727494-18e6-4ad4-b96e-0b248d47aa5e/GCF_012911865.1_ASM1291186v1_genomic.fna.gz | prodigal -d GCF_012911865.1_ASM1291186v1_genomic.fna/cds.fna -a GCF_012911865.1_ASM1291186v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:04:33,131] [INFO] Task succeeded: Prodigal
[2024-01-25 20:04:33,131] [INFO] Task started: HMMsearch
[2024-01-25 20:04:33,131] [INFO] Running command: hmmsearch --tblout GCF_012911865.1_ASM1291186v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea0e732a-8b49-4cf1-97fd-8c0f41ccf914/dqc_reference/reference_markers.hmm GCF_012911865.1_ASM1291186v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:04:33,399] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:04:33,401] [INFO] Found 6/6 markers.
[2024-01-25 20:04:33,452] [INFO] Query marker FASTA was written to GCF_012911865.1_ASM1291186v1_genomic.fna/markers.fasta
[2024-01-25 20:04:33,452] [INFO] Task started: Blastn
[2024-01-25 20:04:33,452] [INFO] Running command: blastn -query GCF_012911865.1_ASM1291186v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea0e732a-8b49-4cf1-97fd-8c0f41ccf914/dqc_reference/reference_markers.fasta -out GCF_012911865.1_ASM1291186v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:04:34,177] [INFO] Task succeeded: Blastn
[2024-01-25 20:04:34,179] [INFO] Selected 21 target genomes.
[2024-01-25 20:04:34,180] [INFO] Target genome list was writen to GCF_012911865.1_ASM1291186v1_genomic.fna/target_genomes.txt
[2024-01-25 20:04:34,196] [INFO] Task started: fastANI
[2024-01-25 20:04:34,196] [INFO] Running command: fastANI --query /var/lib/cwl/stg44727494-18e6-4ad4-b96e-0b248d47aa5e/GCF_012911865.1_ASM1291186v1_genomic.fna.gz --refList GCF_012911865.1_ASM1291186v1_genomic.fna/target_genomes.txt --output GCF_012911865.1_ASM1291186v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:04:51,058] [INFO] Task succeeded: fastANI
[2024-01-25 20:04:51,059] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea0e732a-8b49-4cf1-97fd-8c0f41ccf914/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:04:51,059] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea0e732a-8b49-4cf1-97fd-8c0f41ccf914/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:04:51,071] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:04:51,071] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:04:51,071] [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
Shewanella salipaludis	strain=SHSM-M6	GCA_012911865.1	2723052	2723052	type	True	100.0	1398	1399	95	conclusive
Shewanella putrefaciens	strain=ATCC 8071	GCA_016406325.1	24	24	type	True	79.4603	258	1399	95	below_threshold
Shewanella oncorhynchi	strain=S-1	GCA_012584455.1	2726434	2726434	type	True	79.3603	280	1399	95	below_threshold
Shewanella hafniensis	strain=ATCC BAA-1207	GCA_019655335.1	365590	365590	type	True	79.3226	310	1399	95	below_threshold
Shewanella baltica	strain=NCTC10735	GCA_900456975.1	62322	62322	type	True	79.3073	317	1399	95	below_threshold
Shewanella profunda	strain=DSM 15900	GCA_023283765.1	254793	254793	type	True	79.1518	266	1399	95	below_threshold
Shewanella putrefaciens	strain=NBRC 3908	GCA_001591325.1	24	24	type	True	79.0898	248	1399	95	below_threshold
Shewanella cyperi	strain=FJAT-53720	GCA_017354985.1	2814292	2814292	type	True	78.9811	510	1399	95	below_threshold
Shewanella sedimentimangrovi	strain=FJAT-52962	GCA_017354965.1	2814293	2814293	type	True	78.979	501	1399	95	below_threshold
Shewanella decolorationis	strain=S12	GCA_000485795.1	256839	256839	type	True	78.9774	306	1399	95	below_threshold
Shewanella seohaensis	strain=CCUG 60900	GCA_023283775.1	755175	755175	type	True	78.8327	324	1399	95	below_threshold
Shewanella algae	strain=CECT 5071	GCA_009183365.2	38313	38313	type	True	78.4849	442	1399	95	below_threshold
Shewanella carassii	strain=08MAS2251	GCA_002777975.1	1987584	1987584	type	True	78.4767	400	1399	95	below_threshold
Shewanella carassii	strain=CGMCC 1.16033	GCA_014644375.1	1987584	1987584	type	True	78.4228	406	1399	95	below_threshold
Shewanella algae	strain=NBRC 103173	GCA_001598875.1	38313	38313	type	True	78.3813	424	1399	95	below_threshold
Shewanella chilikensis	strain=CCUG 57101	GCA_023283475.1	558541	558541	type	True	78.352	412	1399	95	below_threshold
Shewanella amazonensis	strain=SB2B	GCA_000015245.1	60478	60478	type	True	78.2681	311	1399	95	below_threshold
Shewanella insulae	strain=JBTF-M18	GCA_009831655.1	2681496	2681496	type	True	78.1967	431	1399	95	below_threshold
Shewanella aquimarina	strain=JCM 12193	GCA_023349185.1	260365	260365	type	True	78.1478	430	1399	95	below_threshold
Shewanella violacea	strain=DSS12	GCA_000091325.1	60217	60217	type	True	77.7028	188	1399	95	below_threshold
Shewanella benthica	strain=DSM 8812	GCA_015069875.1	43661	43661	type	True	77.6872	139	1399	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:04:51,077] [INFO] DFAST Taxonomy check result was written to GCF_012911865.1_ASM1291186v1_genomic.fna/tc_result.tsv
[2024-01-25 20:04:51,077] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:04:51,077] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:04:51,078] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea0e732a-8b49-4cf1-97fd-8c0f41ccf914/dqc_reference/checkm_data
[2024-01-25 20:04:51,079] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:04:51,127] [INFO] Task started: CheckM
[2024-01-25 20:04:51,127] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012911865.1_ASM1291186v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012911865.1_ASM1291186v1_genomic.fna/checkm_input GCF_012911865.1_ASM1291186v1_genomic.fna/checkm_result
[2024-01-25 20:05:25,965] [INFO] Task succeeded: CheckM
[2024-01-25 20:05:25,966] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:05:26,028] [INFO] ===== Completeness check finished =====
[2024-01-25 20:05:26,028] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:05:26,028] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012911865.1_ASM1291186v1_genomic.fna/markers.fasta)
[2024-01-25 20:05:26,029] [INFO] Task started: Blastn
[2024-01-25 20:05:26,029] [INFO] Running command: blastn -query GCF_012911865.1_ASM1291186v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea0e732a-8b49-4cf1-97fd-8c0f41ccf914/dqc_reference/reference_markers_gtdb.fasta -out GCF_012911865.1_ASM1291186v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:27,076] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:27,080] [INFO] Selected 24 target genomes.
[2024-01-25 20:05:27,080] [INFO] Target genome list was writen to GCF_012911865.1_ASM1291186v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:05:27,166] [INFO] Task started: fastANI
[2024-01-25 20:05:27,166] [INFO] Running command: fastANI --query /var/lib/cwl/stg44727494-18e6-4ad4-b96e-0b248d47aa5e/GCF_012911865.1_ASM1291186v1_genomic.fna.gz --refList GCF_012911865.1_ASM1291186v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012911865.1_ASM1291186v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:05:44,638] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:44,653] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:05:44,653] [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
GCF_012911865.1	s__Shewanella sp012911865	100.0	1398	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016406325.1	s__Shewanella putrefaciens	79.4758	258	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.29	98.60	0.96	0.93	12	-
GCF_900456975.1	s__Shewanella baltica	79.3073	317	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.88	96.32	0.89	0.85	16	-
GCF_002966515.1	s__Shewanella sp002966515	79.3072	300	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.53	97.30	0.89	0.86	10	-
GCA_002783505.1	s__Shewanella sp002783505	79.3055	318	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002838165.1	s__Shewanella sp002838165	79.2672	325	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.37	97.32	0.89	0.88	8	-
GCF_900156405.1	s__Shewanella morhuae	79.0581	237	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.45	98.44	0.93	0.93	3	-
GCF_017354985.1	s__Shewanella sp017354985	79.0077	506	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.75	95.81	0.93	0.92	3	-
GCF_000014665.1	s__Shewanella sp000014665	78.9839	325	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.13	97.13	0.94	0.94	2	-
GCF_000485795.1	s__Shewanella decolorationis	78.9647	307	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.60	97.51	0.93	0.92	3	-
GCF_000203935.1	s__Shewanella sp000203935	78.8945	325	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	95.76	95.76	0.86	0.86	2	-
GCF_002777975.1	s__Shewanella carassii	78.4865	399	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009183365.2	s__Shewanella algae	78.4796	445	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.21	97.66	0.95	0.92	87	-
GCF_002836975.1	s__Shewanella indica	78.4408	405	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.7827	98.42	98.01	0.95	0.93	6	-
GCF_000016065.1	s__Shewanella loihica	78.3086	437	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	95.22	95.22	0.91	0.91	2	-
GCF_002836945.1	s__Shewanella chilikensis	78.2593	411	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.7827	99.40	98.79	0.97	0.93	5	-
GCF_000015245.1	s__Shewanella amazonensis	78.2467	313	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000832025.1	s__Shewanella sp000832025	78.2307	417	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000091325.1	s__Shewanella violacea	77.7236	188	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015069875.1	s__Shewanella benthica	77.6872	139	1399	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.81	96.81	0.66	0.66	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:05:44,655] [INFO] GTDB search result was written to GCF_012911865.1_ASM1291186v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:05:44,655] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:05:44,659] [INFO] DFAST_QC result json was written to GCF_012911865.1_ASM1291186v1_genomic.fna/dqc_result.json
[2024-01-25 20:05:44,659] [INFO] DFAST_QC completed!
[2024-01-25 20:05:44,659] [INFO] Total running time: 0h1m24s