[2024-01-24 10:47:40,968] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:40,975] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:40,975] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd2a5653-b4ce-4823-b2a9-cff0ee869b1c/dqc_reference
[2024-01-24 10:47:44,787] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:44,789] [INFO] Task started: Prodigal
[2024-01-24 10:47:44,790] [INFO] Running command: gunzip -c /var/lib/cwl/stg4802ab1b-491b-4428-8129-ba6500790d94/GCF_001652445.1_ASM165244v1_genomic.fna.gz | prodigal -d GCF_001652445.1_ASM165244v1_genomic.fna/cds.fna -a GCF_001652445.1_ASM165244v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:52,389] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:52,390] [INFO] Task started: HMMsearch
[2024-01-24 10:47:52,390] [INFO] Running command: hmmsearch --tblout GCF_001652445.1_ASM165244v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd2a5653-b4ce-4823-b2a9-cff0ee869b1c/dqc_reference/reference_markers.hmm GCF_001652445.1_ASM165244v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:52,681] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:52,683] [INFO] Found 6/6 markers.
[2024-01-24 10:47:52,716] [INFO] Query marker FASTA was written to GCF_001652445.1_ASM165244v1_genomic.fna/markers.fasta
[2024-01-24 10:47:52,716] [INFO] Task started: Blastn
[2024-01-24 10:47:52,716] [INFO] Running command: blastn -query GCF_001652445.1_ASM165244v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd2a5653-b4ce-4823-b2a9-cff0ee869b1c/dqc_reference/reference_markers.fasta -out GCF_001652445.1_ASM165244v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:53,465] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:53,471] [INFO] Selected 18 target genomes.
[2024-01-24 10:47:53,471] [INFO] Target genome list was writen to GCF_001652445.1_ASM165244v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:53,482] [INFO] Task started: fastANI
[2024-01-24 10:47:53,483] [INFO] Running command: fastANI --query /var/lib/cwl/stg4802ab1b-491b-4428-8129-ba6500790d94/GCF_001652445.1_ASM165244v1_genomic.fna.gz --refList GCF_001652445.1_ASM165244v1_genomic.fna/target_genomes.txt --output GCF_001652445.1_ASM165244v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:06,590] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:06,591] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd2a5653-b4ce-4823-b2a9-cff0ee869b1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:06,591] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd2a5653-b4ce-4823-b2a9-cff0ee869b1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:06,604] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:48:06,604] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:06,604] [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
Thalassotalea crassostreae	strain=LPB0090	GCA_001652445.1	1763536	1763536	type	True	100.0	1245	1248	95	conclusive
Thalassotalea crassostreae	strain=LPB0090	GCA_001831495.1	1763536	1763536	type	True	99.9966	1246	1248	95	conclusive
Thalassotalea mangrovi	strain=ZS-4	GCA_005116735.1	2572245	2572245	type	True	78.5324	102	1248	95	below_threshold
Litorilituus sediminis	strain=JCM 17549	GCA_004295665.1	718192	718192	type	True	78.3481	134	1248	95	below_threshold
Thalassotalea agarivorans	strain=DSM 19706	GCA_900111755.1	349064	349064	type	True	78.3458	101	1248	95	below_threshold
Cognaticolwellia mytili	strain=KCTC 52417	GCA_002104475.1	1888913	1888913	type	True	78.1059	139	1248	95	below_threshold
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	78.0663	132	1248	95	below_threshold
Colwellia demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	78.021	117	1248	95	below_threshold
Thalassotalea marina	strain=KCTC 42731	GCA_014656435.1	1673741	1673741	type	True	78.0122	115	1248	95	below_threshold
Thalassotalea profundi	strain=CGMCC 1.15922	GCA_014653195.1	2036687	2036687	type	True	77.7481	119	1248	95	below_threshold
Thalassotalea piscium	strain=DSM 26287	GCA_014207645.1	1230533	1230533	type	True	77.7176	113	1248	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	77.6413	114	1248	95	below_threshold
Colwellia piezophila	strain=ATCC BAA-637	GCA_000378625.1	211668	211668	type	True	77.5163	133	1248	95	below_threshold
Photobacterium phosphoreum	strain=ATCC 11040	GCA_000949955.1	659	659	type	True	76.3579	50	1248	95	below_threshold
Photobacterium toruni	strain=CECT 9189	GCA_024529955.1	1935446	1935446	type	True	76.1677	63	1248	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:06,606] [INFO] DFAST Taxonomy check result was written to GCF_001652445.1_ASM165244v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:06,607] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:06,607] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:06,607] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd2a5653-b4ce-4823-b2a9-cff0ee869b1c/dqc_reference/checkm_data
[2024-01-24 10:48:06,609] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:06,647] [INFO] Task started: CheckM
[2024-01-24 10:48:06,647] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001652445.1_ASM165244v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001652445.1_ASM165244v1_genomic.fna/checkm_input GCF_001652445.1_ASM165244v1_genomic.fna/checkm_result
[2024-01-24 10:48:34,875] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:34,877] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:34,899] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:34,899] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:34,900] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001652445.1_ASM165244v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:34,900] [INFO] Task started: Blastn
[2024-01-24 10:48:34,901] [INFO] Running command: blastn -query GCF_001652445.1_ASM165244v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd2a5653-b4ce-4823-b2a9-cff0ee869b1c/dqc_reference/reference_markers_gtdb.fasta -out GCF_001652445.1_ASM165244v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:36,113] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:36,116] [INFO] Selected 19 target genomes.
[2024-01-24 10:48:36,116] [INFO] Target genome list was writen to GCF_001652445.1_ASM165244v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:36,142] [INFO] Task started: fastANI
[2024-01-24 10:48:36,143] [INFO] Running command: fastANI --query /var/lib/cwl/stg4802ab1b-491b-4428-8129-ba6500790d94/GCF_001652445.1_ASM165244v1_genomic.fna.gz --refList GCF_001652445.1_ASM165244v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001652445.1_ASM165244v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:49,921] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:49,938] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:49,939] [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_001831495.1	s__Thalassotalea_A crassostreae	99.9966	1246	1248	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_A	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_002162925.1	s__Thalassotalea_A sp002162925	79.0849	225	1248	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764205.1	s__Thalassotalea_A sp000764205	78.9704	244	1248	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097525.1	s__Thalassotalea_A sp007097525	78.968	313	1248	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860585.1	s__Colwellia sp018860585	78.6098	112	1248	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005116735.1	s__Thalassotalea_A mangrovi	78.5324	102	1248	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004752005.1	s__Thalassotalea_A sp004752005	78.4199	216	1248	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_A	95.0	95.63	95.63	0.92	0.92	2	-
GCF_900111755.1	s__Thalassotalea_D agarivorans	78.3588	100	1248	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004295665.1	s__Litorilituus sediminis	78.3485	134	1248	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Litorilituus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007197775.1	s__Thalassotalea_A sp007197775	78.3447	131	1248	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390335.1	s__Thalassotalea euphylliae_B	78.1891	104	1248	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002000025.1	s__Cognaticolwellia aestuarii	78.0548	139	1248	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007954275.1	s__Colwellia demingiae	78.0475	116	1248	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003333305.1	s__Colwellia aromaticivorans	77.9468	106	1248	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012325.1	s__Colwellia psychrerythraea_A	77.873	127	1248	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	98.43	98.43	0.88	0.88	2	-
GCF_014076845.1	s__Colwellia_A sp014076845	77.852	117	1248	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	99.15	95.49	0.95	0.86	8	-
GCF_000378625.1	s__Colwellia piezophila	77.5114	134	1248	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002163005.1	s__Colwellia psychrerythraea_C	77.4872	118	1248	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003354085.1	s__Cognaticolwellia sp003354085	76.9132	128	1248	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:49,940] [INFO] GTDB search result was written to GCF_001652445.1_ASM165244v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:49,942] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:49,946] [INFO] DFAST_QC result json was written to GCF_001652445.1_ASM165244v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:49,946] [INFO] DFAST_QC completed!
[2024-01-24 10:48:49,947] [INFO] Total running time: 0h1m9s