[2024-01-24 10:47:06,587] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,596] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,596] [INFO] DQC Reference Directory: /var/lib/cwl/stga226332c-79b6-4640-8975-5f6c8172908a/dqc_reference
[2024-01-24 10:47:12,679] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,828] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,831] [INFO] Running command: gunzip -c /var/lib/cwl/stgcd809426-74c0-452b-a749-20359728a3ec/GCF_005843985.1_ASM584398v1_genomic.fna.gz | prodigal -d GCF_005843985.1_ASM584398v1_genomic.fna/cds.fna -a GCF_005843985.1_ASM584398v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:15,494] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:15,494] [INFO] Task started: HMMsearch
[2024-01-24 10:47:15,495] [INFO] Running command: hmmsearch --tblout GCF_005843985.1_ASM584398v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga226332c-79b6-4640-8975-5f6c8172908a/dqc_reference/reference_markers.hmm GCF_005843985.1_ASM584398v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:15,868] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:15,870] [INFO] Found 6/6 markers.
[2024-01-24 10:47:15,888] [INFO] Query marker FASTA was written to GCF_005843985.1_ASM584398v1_genomic.fna/markers.fasta
[2024-01-24 10:47:16,194] [INFO] Task started: Blastn
[2024-01-24 10:47:16,194] [INFO] Running command: blastn -query GCF_005843985.1_ASM584398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga226332c-79b6-4640-8975-5f6c8172908a/dqc_reference/reference_markers.fasta -out GCF_005843985.1_ASM584398v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:19,638] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:19,642] [INFO] Selected 12 target genomes.
[2024-01-24 10:47:19,642] [INFO] Target genome list was writen to GCF_005843985.1_ASM584398v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:20,340] [INFO] Task started: fastANI
[2024-01-24 10:47:20,341] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd809426-74c0-452b-a749-20359728a3ec/GCF_005843985.1_ASM584398v1_genomic.fna.gz --refList GCF_005843985.1_ASM584398v1_genomic.fna/target_genomes.txt --output GCF_005843985.1_ASM584398v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:25,135] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:25,136] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga226332c-79b6-4640-8975-5f6c8172908a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:25,136] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga226332c-79b6-4640-8975-5f6c8172908a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:25,147] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:47:25,147] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:25,148] [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
Caminibacter mediatlanticus	strain=TB-2	GCA_005843985.1	291048	291048	type	True	100.0	561	561	95	conclusive
Caminibacter mediatlanticus	strain=TB-2	GCA_000170735.1	291048	291048	type	True	98.7714	504	561	95	conclusive
Lebetimonas natsushimae	strain=HS1857	GCA_002335445.1	1936991	1936991	type	True	78.2927	265	561	95	below_threshold
Caminibacter pacificus	strain=TB6	GCA_005083985.2	1424653	1424653	type	True	78.2247	223	561	95	below_threshold
Caminibacter pacificus	strain=DSM 27783	GCA_003752135.1	1424653	1424653	type	True	77.9147	215	561	95	below_threshold
Aliarcobacter lanthieri	strain=LMG 28516	GCA_013201625.1	1355374	1355374	type	True	76.8692	105	561	95	below_threshold
Aliarcobacter butzleri	strain=RM4018	GCA_000014025.1	28197	28197	type	True	76.3968	102	561	95	below_threshold
Aliarcobacter lanthieri	strain=LMG 28516	GCA_024584095.1	1355374	1355374	type	True	76.1101	97	561	95	below_threshold
Arcobacter ellisii	strain=LMG 26155	GCA_003544915.1	913109	913109	type	True	76.056	111	561	95	below_threshold
[Arcobacter] porcinus	strain=LMG 24487	GCA_024584075.1	1935204	1935204	type	True	75.8064	104	561	95	below_threshold
Arcobacter caeni	strain=RW17-10	GCA_003063245.1	1912877	1912877	type	True	75.6814	99	561	95	below_threshold
Arcobacter ellisii	strain=CECT 7837	GCA_004115815.1	913109	913109	type	True	75.4484	104	561	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:25,149] [INFO] DFAST Taxonomy check result was written to GCF_005843985.1_ASM584398v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:25,152] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:25,152] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:25,152] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga226332c-79b6-4640-8975-5f6c8172908a/dqc_reference/checkm_data
[2024-01-24 10:47:25,153] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:25,179] [INFO] Task started: CheckM
[2024-01-24 10:47:25,179] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005843985.1_ASM584398v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005843985.1_ASM584398v1_genomic.fna/checkm_input GCF_005843985.1_ASM584398v1_genomic.fna/checkm_result
[2024-01-24 10:47:44,131] [INFO] Task succeeded: CheckM
[2024-01-24 10:47:44,132] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:47:44,172] [INFO] ===== Completeness check finished =====
[2024-01-24 10:47:44,173] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:47:44,173] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005843985.1_ASM584398v1_genomic.fna/markers.fasta)
[2024-01-24 10:47:44,174] [INFO] Task started: Blastn
[2024-01-24 10:47:44,174] [INFO] Running command: blastn -query GCF_005843985.1_ASM584398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga226332c-79b6-4640-8975-5f6c8172908a/dqc_reference/reference_markers_gtdb.fasta -out GCF_005843985.1_ASM584398v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:47,790] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:47,794] [INFO] Selected 18 target genomes.
[2024-01-24 10:47:47,794] [INFO] Target genome list was writen to GCF_005843985.1_ASM584398v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:47:47,938] [INFO] Task started: fastANI
[2024-01-24 10:47:47,938] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd809426-74c0-452b-a749-20359728a3ec/GCF_005843985.1_ASM584398v1_genomic.fna.gz --refList GCF_005843985.1_ASM584398v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005843985.1_ASM584398v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:47:55,135] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:55,149] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:47:55,150] [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_005843985.1	s__Caminibacter mediatlanticus	100.0	561	561	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Nautiliales;f__Nautiliaceae;g__Caminibacter	95.0	98.80	98.80	0.94	0.94	2	conclusive
GCF_002335445.1	s__Lebetimonas natsushimae	78.3414	263	561	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Nautiliales;f__Nautiliaceae;g__Lebetimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000021725.1	s__Nautilia profundicola	78.1783	176	561	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Nautiliales;f__Nautiliaceae;g__Nautilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004006315.1	s__Nautilia profundicola_A	77.9645	144	561	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Nautiliales;f__Nautiliaceae;g__Nautilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003752135.1	s__Cetia pacifica	77.9357	216	561	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Nautiliales;f__Nautiliaceae;g__Cetia	95.0	99.26	98.54	0.96	0.92	3	-
GCF_013201625.1	s__Aliarcobacter lanthieri	76.6591	103	561	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.15	95.77	0.93	0.89	6	-
GCF_004214815.1	s__Aliarcobacter thereius	76.4746	92	561	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.14	98.62	0.93	0.89	8	-
GCF_004299785.2	s__Aliarcobacter porcinus	76.2185	113	561	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.76	98.06	0.91	0.88	6	-
GCF_003544915.1	s__Aliarcobacter ellisii	75.9846	108	561	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.73	97.46	0.92	0.84	3	-
GCF_002993025.1	s__Aliarcobacter cryaerophilus_B	75.8612	86	561	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.88	97.88	0.90	0.90	2	-
GCF_003063245.1	s__Aliarcobacter caeni	75.692	98	561	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215915.1	s__NORP36 sp013215915	75.5829	95	561	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__NORP36	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013388565.1	s__JACAEZ01 sp013388565	75.5501	50	561	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__JACAEZ01;g__JACAEZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215985.1	s__NORP36 sp013215985	75.526	89	561	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__NORP36	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016599045.1	s__Campylobacter_D sp016599045	75.3849	74	561	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Campylobacteraceae;g__Campylobacter_D	95.0	99.00	98.98	0.95	0.93	3	-
GCA_004116725.1	s__Malaciobacter sp004116725	75.3804	109	561	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744535.1	s__BB28 sp016744535	75.2454	130	561	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__BB28;g__BB28	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:47:55,151] [INFO] GTDB search result was written to GCF_005843985.1_ASM584398v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:47:55,152] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:47:55,156] [INFO] DFAST_QC result json was written to GCF_005843985.1_ASM584398v1_genomic.fna/dqc_result.json
[2024-01-24 10:47:55,156] [INFO] DFAST_QC completed!
[2024-01-24 10:47:55,156] [INFO] Total running time: 0h0m49s