[2024-01-24 11:13:04,599] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:13:04,600] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:13:04,601] [INFO] DQC Reference Directory: /var/lib/cwl/stg1ece6799-1658-43c0-a655-bf28dc849430/dqc_reference
[2024-01-24 11:13:05,830] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:13:05,831] [INFO] Task started: Prodigal
[2024-01-24 11:13:05,831] [INFO] Running command: gunzip -c /var/lib/cwl/stg65e50f2a-ad85-42e2-b4ba-b7efd23daef2/GCF_014384885.1_ASM1438488v1_genomic.fna.gz | prodigal -d GCF_014384885.1_ASM1438488v1_genomic.fna/cds.fna -a GCF_014384885.1_ASM1438488v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:14,318] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:14,319] [INFO] Task started: HMMsearch
[2024-01-24 11:13:14,319] [INFO] Running command: hmmsearch --tblout GCF_014384885.1_ASM1438488v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1ece6799-1658-43c0-a655-bf28dc849430/dqc_reference/reference_markers.hmm GCF_014384885.1_ASM1438488v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:14,633] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:14,634] [INFO] Found 6/6 markers.
[2024-01-24 11:13:14,662] [INFO] Query marker FASTA was written to GCF_014384885.1_ASM1438488v1_genomic.fna/markers.fasta
[2024-01-24 11:13:14,662] [INFO] Task started: Blastn
[2024-01-24 11:13:14,662] [INFO] Running command: blastn -query GCF_014384885.1_ASM1438488v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ece6799-1658-43c0-a655-bf28dc849430/dqc_reference/reference_markers.fasta -out GCF_014384885.1_ASM1438488v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:15,429] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:15,433] [INFO] Selected 19 target genomes.
[2024-01-24 11:13:15,433] [INFO] Target genome list was writen to GCF_014384885.1_ASM1438488v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:15,452] [INFO] Task started: fastANI
[2024-01-24 11:13:15,453] [INFO] Running command: fastANI --query /var/lib/cwl/stg65e50f2a-ad85-42e2-b4ba-b7efd23daef2/GCF_014384885.1_ASM1438488v1_genomic.fna.gz --refList GCF_014384885.1_ASM1438488v1_genomic.fna/target_genomes.txt --output GCF_014384885.1_ASM1438488v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:26,751] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:26,752] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1ece6799-1658-43c0-a655-bf28dc849430/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:26,753] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1ece6799-1658-43c0-a655-bf28dc849430/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:26,768] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:26,768] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:26,768] [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
Ligaoa zhengdingensis	strain=NSJ-31	GCA_014384885.1	2763658	2763658	type	True	100.0	926	932	95	conclusive
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	83.0469	66	932	95	below_threshold
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	81.2383	89	932	95	below_threshold
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	80.9898	87	932	95	below_threshold
Angelakisella massiliensis	strain=Marseille-P3217	GCA_900104675.1	1871018	1871018	type	True	80.8824	113	932	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	78.1411	88	932	95	below_threshold
Provencibacterium massiliense	strain=Marseille-P2780	GCA_900169495.1	1841868	1841868	type	True	77.9282	173	932	95	below_threshold
Anaerotruncus massiliensis	strain=AT3	GCA_900199635.1	1673720	1673720	type	True	77.615	178	932	95	below_threshold
Hydrogenoanaerobacterium saccharovorans	strain=DSM 24774	GCA_003814745.1	474960	474960	type	True	77.6125	85	932	95	below_threshold
Hydrogenoanaerobacterium saccharovorans	strain=CGMCC 1.5070	GCA_900110045.1	474960	474960	type	True	77.5132	87	932	95	below_threshold
Anaerotruncus rubiinfantis	strain=MT15	GCA_900078395.1	1720200	1720200	type	True	77.4688	108	932	95	below_threshold
Phocea massiliensis	strain=Marseille-P2769	GCA_900104615.1	1841867	1841867	type	True	77.0942	98	932	95	below_threshold
Marasmitruncus massiliensis	strain=Marseille-P3646	GCA_900186535.1	1944642	1944642	type	True	76.7875	56	932	95	below_threshold
Acetanaerobacterium elongatum	strain=CGMCC 1.5012	GCA_900103835.1	258515	258515	type	True	76.6075	64	932	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:26,770] [INFO] DFAST Taxonomy check result was written to GCF_014384885.1_ASM1438488v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:26,771] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:26,771] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:26,772] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1ece6799-1658-43c0-a655-bf28dc849430/dqc_reference/checkm_data
[2024-01-24 11:13:26,773] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:26,804] [INFO] Task started: CheckM
[2024-01-24 11:13:26,804] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014384885.1_ASM1438488v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014384885.1_ASM1438488v1_genomic.fna/checkm_input GCF_014384885.1_ASM1438488v1_genomic.fna/checkm_result
[2024-01-24 11:13:56,734] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:56,736] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:56,757] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:56,757] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:56,758] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014384885.1_ASM1438488v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:56,758] [INFO] Task started: Blastn
[2024-01-24 11:13:56,758] [INFO] Running command: blastn -query GCF_014384885.1_ASM1438488v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ece6799-1658-43c0-a655-bf28dc849430/dqc_reference/reference_markers_gtdb.fasta -out GCF_014384885.1_ASM1438488v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:58,183] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:58,188] [INFO] Selected 25 target genomes.
[2024-01-24 11:13:58,188] [INFO] Target genome list was writen to GCF_014384885.1_ASM1438488v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:58,223] [INFO] Task started: fastANI
[2024-01-24 11:13:58,224] [INFO] Running command: fastANI --query /var/lib/cwl/stg65e50f2a-ad85-42e2-b4ba-b7efd23daef2/GCF_014384885.1_ASM1438488v1_genomic.fna.gz --refList GCF_014384885.1_ASM1438488v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014384885.1_ASM1438488v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:08,984] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:09,003] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:09,003] [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_014384885.1	s__Hydrogenoanaerobacterium sp014384885	100.0	926	932	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Hydrogenoanaerobacterium	95.0	98.59	98.59	0.91	0.91	2	conclusive
GCF_900199635.1	s__Anaerotruncus massiliensis	77.615	178	932	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	98.56	98.01	0.95	0.93	6	-
GCF_003814745.1	s__Hydrogenoanaerobacterium saccharovorans	77.6125	85	932	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Hydrogenoanaerobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900078395.1	s__Anaerotruncus rubiinfantis	77.4688	108	932	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	99.23	99.21	0.89	0.86	5	-
GCA_004340125.1	s__Harryflintia acetispora	77.3788	158	932	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Harryflintia	95.0	98.73	98.54	0.92	0.90	6	-
GCF_904419105.1	s__Avimicrobium faecavium	77.1257	69	932	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Avimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904398325.1	s__Neoruminococcus faecicola	77.0926	97	932	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Neoruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004558145.1	s__Fournierella excrementavium	76.9981	90	932	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Fournierella	95.0	97.60	97.45	0.91	0.87	5	-
GCA_019114825.1	s__Anaerotruncus excrementipullorum	76.9896	98	932	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	99.88	99.88	0.94	0.94	2	-
GCA_900760305.1	s__UMGS856 sp900760305	76.8723	61	932	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UMGS856	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585525.1	s__Angelakisella sp910585525	76.8452	81	932	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Angelakisella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905233755.1	s__Ruminococcus_E sp905233755	76.8161	56	932	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904387055.1	s__Heteroruminococcus faecigallinarum	76.7906	89	932	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Heteroruminococcus	95.0	99.97	99.97	0.96	0.96	2	-
GCA_905192745.1	s__Avimonas sp900551425	76.7878	57	932	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Avimonas	95.0	99.85	99.85	0.95	0.95	2	-
GCA_018715025.1	s__Caccousia avistercoris	76.7763	61	932	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caccousia	95.0	98.39	98.39	0.86	0.86	2	-
GCA_904420255.1	s__Angelakisella sp904420255	76.7568	76	932	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Angelakisella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015667585.1	s__Anaeromassilibacillus sp015667585	76.7532	78	932	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Anaeromassilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900761965.1	s__Avimicrobium sp900761965	76.6954	50	932	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Avimicrobium	95.0	98.03	98.03	0.92	0.92	2	-
GCF_016901815.1	s__Avimicrobium caecorum	76.3172	55	932	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Avimicrobium	95.0	98.00	97.74	0.94	0.92	7	-
GCA_910585535.1	s__Angelakisella sp910585535	76.1406	60	932	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Angelakisella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:09,005] [INFO] GTDB search result was written to GCF_014384885.1_ASM1438488v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:09,005] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:09,009] [INFO] DFAST_QC result json was written to GCF_014384885.1_ASM1438488v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:09,009] [INFO] DFAST_QC completed!
[2024-01-24 11:14:09,009] [INFO] Total running time: 0h1m4s