[2024-01-25 19:24:45,019] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:24:45,020] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:24:45,021] [INFO] DQC Reference Directory: /var/lib/cwl/stg9699d155-d56f-4da3-8c95-30634d44f25a/dqc_reference
[2024-01-25 19:24:48,241] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:24:48,242] [INFO] Task started: Prodigal
[2024-01-25 19:24:48,242] [INFO] Running command: gunzip -c /var/lib/cwl/stg13532177-c996-48cf-9ee6-695dd69e15f6/GCF_016027375.1_ASM1602737v1_genomic.fna.gz | prodigal -d GCF_016027375.1_ASM1602737v1_genomic.fna/cds.fna -a GCF_016027375.1_ASM1602737v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:24:52,476] [INFO] Task succeeded: Prodigal
[2024-01-25 19:24:52,477] [INFO] Task started: HMMsearch
[2024-01-25 19:24:52,477] [INFO] Running command: hmmsearch --tblout GCF_016027375.1_ASM1602737v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9699d155-d56f-4da3-8c95-30634d44f25a/dqc_reference/reference_markers.hmm GCF_016027375.1_ASM1602737v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:24:52,793] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:24:52,794] [INFO] Found 6/6 markers.
[2024-01-25 19:24:52,820] [INFO] Query marker FASTA was written to GCF_016027375.1_ASM1602737v1_genomic.fna/markers.fasta
[2024-01-25 19:24:52,821] [INFO] Task started: Blastn
[2024-01-25 19:24:52,821] [INFO] Running command: blastn -query GCF_016027375.1_ASM1602737v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9699d155-d56f-4da3-8c95-30634d44f25a/dqc_reference/reference_markers.fasta -out GCF_016027375.1_ASM1602737v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:24:55,505] [INFO] Task succeeded: Blastn
[2024-01-25 19:24:55,507] [INFO] Selected 17 target genomes.
[2024-01-25 19:24:55,508] [INFO] Target genome list was writen to GCF_016027375.1_ASM1602737v1_genomic.fna/target_genomes.txt
[2024-01-25 19:24:55,981] [INFO] Task started: fastANI
[2024-01-25 19:24:55,981] [INFO] Running command: fastANI --query /var/lib/cwl/stg13532177-c996-48cf-9ee6-695dd69e15f6/GCF_016027375.1_ASM1602737v1_genomic.fna.gz --refList GCF_016027375.1_ASM1602737v1_genomic.fna/target_genomes.txt --output GCF_016027375.1_ASM1602737v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:25:08,083] [INFO] Task succeeded: fastANI
[2024-01-25 19:25:08,084] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9699d155-d56f-4da3-8c95-30634d44f25a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:25:08,084] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9699d155-d56f-4da3-8c95-30634d44f25a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:25:08,095] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:25:08,095] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:25:08,096] [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
Clostridium perfringens	strain=FDAARGOS_903	GCA_016027375.1	1502	1502	type	True	100.0	1118	1118	95	conclusive
Clostridium perfringens	strain=ATCC 13124	GCA_000013285.1	1502	1502	type	True	98.9286	1024	1118	95	conclusive
Clostridium massiliamazoniense	strain=ND2	GCA_001403635.1	1347366	1347366	type	True	78.5847	308	1118	95	below_threshold
Clostridium mediterraneense	strain=Marseille-P2434	GCA_900091705.1	1805472	1805472	type	True	78.5546	269	1118	95	below_threshold
Clostridium tarantellae	strain=DSM 3997	GCA_009295725.1	39493	39493	type	True	78.5261	360	1118	95	below_threshold
Clostridium fallax	strain=NCTC8380	GCA_900461065.1	1533	1533	type	True	78.4298	283	1118	95	below_threshold
Sarcina ventriculi	strain=NCTC12966	GCA_900456775.1	1267	1267	type	True	78.3163	245	1118	95	below_threshold
Clostridium chauvoei	strain=DSM 7528	GCA_002327185.1	46867	46867	type	True	78.0891	270	1118	95	below_threshold
Clostridium fallax	strain=DSM 2631	GCA_900129365.1	1533	1533	type	True	77.7847	271	1118	95	below_threshold
Clostridium celatum	strain=DSM 1785	GCA_000320405.1	36834	36834	type	True	77.5628	226	1118	95	below_threshold
Clostridium gelidum	strain=C5S11	GCA_019977655.1	704125	704125	type	True	77.4318	221	1118	95	below_threshold
Clostridium cagae	strain=Marseille-P4344	GCA_900290265.1	2080751	2080751	type	True	77.3049	232	1118	95	below_threshold
Clostridium tertium	strain=DSM 2485	GCA_017873245.1	1559	1559	type	True	77.1638	243	1118	95	below_threshold
Clostridium felsineum	strain=DSM 794	GCA_002006355.2	36839	36839	type	True	76.914	162	1118	95	below_threshold
Clostridium felsineum	strain=DSM 7320	GCA_002006215.2	36839	36839	type	True	76.8752	163	1118	95	below_threshold
Clostridium felsineum	strain=DSM 793	GCA_002006235.2	36839	36839	type	True	76.726	173	1118	95	below_threshold
Abyssisolibacter fermentans	strain=MCWD3	GCA_001559865.1	1766203	1766203	type	True	74.9283	85	1118	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:25:08,097] [INFO] DFAST Taxonomy check result was written to GCF_016027375.1_ASM1602737v1_genomic.fna/tc_result.tsv
[2024-01-25 19:25:08,098] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:25:08,098] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:25:08,098] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9699d155-d56f-4da3-8c95-30634d44f25a/dqc_reference/checkm_data
[2024-01-25 19:25:08,099] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:25:08,132] [INFO] Task started: CheckM
[2024-01-25 19:25:08,132] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016027375.1_ASM1602737v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016027375.1_ASM1602737v1_genomic.fna/checkm_input GCF_016027375.1_ASM1602737v1_genomic.fna/checkm_result
[2024-01-25 19:25:26,687] [INFO] Task succeeded: CheckM
[2024-01-25 19:25:26,688] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:25:26,709] [INFO] ===== Completeness check finished =====
[2024-01-25 19:25:26,710] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:25:26,710] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016027375.1_ASM1602737v1_genomic.fna/markers.fasta)
[2024-01-25 19:25:26,711] [INFO] Task started: Blastn
[2024-01-25 19:25:26,711] [INFO] Running command: blastn -query GCF_016027375.1_ASM1602737v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9699d155-d56f-4da3-8c95-30634d44f25a/dqc_reference/reference_markers_gtdb.fasta -out GCF_016027375.1_ASM1602737v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:25:27,490] [INFO] Task succeeded: Blastn
[2024-01-25 19:25:27,494] [INFO] Selected 19 target genomes.
[2024-01-25 19:25:27,494] [INFO] Target genome list was writen to GCF_016027375.1_ASM1602737v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:25:27,538] [INFO] Task started: fastANI
[2024-01-25 19:25:27,538] [INFO] Running command: fastANI --query /var/lib/cwl/stg13532177-c996-48cf-9ee6-695dd69e15f6/GCF_016027375.1_ASM1602737v1_genomic.fna.gz --refList GCF_016027375.1_ASM1602737v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016027375.1_ASM1602737v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:25:38,943] [INFO] Task succeeded: fastANI
[2024-01-25 19:25:38,955] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:25:38,955] [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_000013285.1	s__Clostridium_P perfringens	98.9283	1024	1118	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P	95.0	98.05	95.74	0.91	0.81	315	conclusive
GCF_900091705.1	s__Clostridium_P mediterraneense	78.5725	268	1118	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P	95.0	100.00	100.00	0.99	0.99	2	-
GCF_009295725.1	s__Clostridium_P tarantellae	78.5112	362	1118	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001403635.1	s__Clostridium_P massiliamazoniense	78.459	309	1118	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900456775.1	s__Clostridium_P ventriculi	78.2809	245	1118	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_P	95.0	98.93	98.34	0.95	0.94	8	-
GCF_002327185.1	s__Clostridium chauvoei	78.0856	276	1118	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.96	99.88	0.99	0.99	5	-
GCF_900129365.1	s__Clostridium_AH fallax	77.7486	272	1118	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_AH	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000498355.1	s__Clostridium sp000498355	77.6949	310	1118	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015555905.1	s__Clostridium sp015555905	77.6658	219	1118	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.95	98.95	0.73	0.73	2	-
GCF_001735765.2	s__Clostridium taeniosporum	77.6021	262	1118	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900547475.1	s__Clostridium sp900547475	77.52	271	1118	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	96.47	95.30	0.88	0.84	3	-
GCF_015667795.1	s__Clostridium sp015667795	77.3768	278	1118	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017435645.1	s__Clostridium sp017435645	77.232	116	1118	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543325.1	s__Clostridium sp900543325	77.2233	218	1118	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000435835.1	s__Clostridium sp000435835	77.1979	177	1118	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	99.44	99.22	0.92	0.88	4	-
GCF_017873245.1	s__Clostridium tertium	77.1631	244	1118	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	98.32	97.37	0.91	0.89	19	-
GCF_000424205.1	s__Clostridium_X cadaveris	77.1276	150	1118	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_X	95.0	99.52	99.40	0.92	0.82	7	-
GCA_015058405.1	s__Clostridium sp015058405	76.8756	206	1118	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015058375.1	s__Clostridium sp015058375	76.8674	120	1118	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:25:38,956] [INFO] GTDB search result was written to GCF_016027375.1_ASM1602737v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:25:38,957] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:25:38,962] [INFO] DFAST_QC result json was written to GCF_016027375.1_ASM1602737v1_genomic.fna/dqc_result.json
[2024-01-25 19:25:38,963] [INFO] DFAST_QC completed!
[2024-01-25 19:25:38,963] [INFO] Total running time: 0h0m54s