[2023-06-29 10:49:34,788] [INFO] DFAST_QC pipeline started.
[2023-06-29 10:49:34,790] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 10:49:34,790] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d6e57c2-3fc7-45ed-8230-862e4d904045/dqc_reference
[2023-06-29 10:49:36,291] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 10:49:36,292] [INFO] Task started: Prodigal
[2023-06-29 10:49:36,292] [INFO] Running command: gunzip -c /var/lib/cwl/stgc773fcfe-1905-47c6-b58d-0a978f0df14c/GCA_020718155.1_ASM2071815v1_genomic.fna.gz | prodigal -d GCA_020718155.1_ASM2071815v1_genomic.fna/cds.fna -a GCA_020718155.1_ASM2071815v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 10:49:39,857] [INFO] Task succeeded: Prodigal
[2023-06-29 10:49:39,858] [INFO] Task started: HMMsearch
[2023-06-29 10:49:39,858] [INFO] Running command: hmmsearch --tblout GCA_020718155.1_ASM2071815v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d6e57c2-3fc7-45ed-8230-862e4d904045/dqc_reference/reference_markers.hmm GCA_020718155.1_ASM2071815v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 10:49:40,110] [INFO] Task succeeded: HMMsearch
[2023-06-29 10:49:40,111] [INFO] Found 6/6 markers.
[2023-06-29 10:49:40,137] [INFO] Query marker FASTA was written to GCA_020718155.1_ASM2071815v1_genomic.fna/markers.fasta
[2023-06-29 10:49:40,137] [INFO] Task started: Blastn
[2023-06-29 10:49:40,137] [INFO] Running command: blastn -query GCA_020718155.1_ASM2071815v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d6e57c2-3fc7-45ed-8230-862e4d904045/dqc_reference/reference_markers.fasta -out GCA_020718155.1_ASM2071815v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 10:49:40,740] [INFO] Task succeeded: Blastn
[2023-06-29 10:49:40,745] [INFO] Selected 28 target genomes.
[2023-06-29 10:49:40,746] [INFO] Target genome list was writen to GCA_020718155.1_ASM2071815v1_genomic.fna/target_genomes.txt
[2023-06-29 10:49:40,750] [INFO] Task started: fastANI
[2023-06-29 10:49:40,751] [INFO] Running command: fastANI --query /var/lib/cwl/stgc773fcfe-1905-47c6-b58d-0a978f0df14c/GCA_020718155.1_ASM2071815v1_genomic.fna.gz --refList GCA_020718155.1_ASM2071815v1_genomic.fna/target_genomes.txt --output GCA_020718155.1_ASM2071815v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 10:49:51,090] [INFO] Task succeeded: fastANI
[2023-06-29 10:49:51,090] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d6e57c2-3fc7-45ed-8230-862e4d904045/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 10:49:51,091] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d6e57c2-3fc7-45ed-8230-862e4d904045/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 10:49:51,115] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 10:49:51,115] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 10:49:51,115] [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
Arcobacter aquimarinus	strain=W63	GCA_013177635.1	1315211	1315211	type	True	77.5071	132	502	95	below_threshold
Arcobacter aquimarinus	strain=CECT 8442	GCA_004115795.1	1315211	1315211	type	True	77.4821	124	502	95	below_threshold
Arcobacter cloacae	strain=LMG 26153	GCA_013201935.1	1054034	1054034	type	True	77.3897	142	502	95	below_threshold
Arcobacter cloacae	strain=CECT 7834	GCA_004115805.1	1054034	1054034	type	True	77.3599	140	502	95	below_threshold
Aliarcobacter lanthieri	strain=LMG 28516	GCA_013201625.1	1355374	1355374	type	True	77.267	113	502	95	below_threshold
Arcobacter suis	strain=CECT 7833	GCA_003544815.1	1278212	1278212	type	True	77.213	118	502	95	below_threshold
Aliarcobacter butzleri	strain=NCTC 12481	GCA_900187115.1	28197	28197	type	True	77.2046	119	502	95	below_threshold
Aliarcobacter cryaerophilus	strain=ATCC 43158	GCA_003660105.1	28198	28198	suspected-type	True	77.1882	112	502	95	below_threshold
Aliarcobacter butzleri	strain=RM4018	GCA_000014025.1	28197	28197	type	True	77.1615	120	502	95	below_threshold
Arcobacter ellisii	strain=CECT 7837	GCA_004115815.1	913109	913109	type	True	77.159	135	502	95	below_threshold
Arcobacter suis	strain=CECT7833	GCA_004023465.1	1278212	1278212	type	True	77.1483	114	502	95	below_threshold
Aliarcobacter cryaerophilus	strain=LMG 24291	GCA_002992955.1	28198	28198	suspected-type	True	77.1279	110	502	95	below_threshold
Aliarcobacter butzleri	strain=LMG 10828	GCA_024584145.1	28197	28197	type	True	77.1196	120	502	95	below_threshold
Aliarcobacter cryaerophilus	strain=LMG 9904	GCA_006165035.1	28198	28198	suspected-type	True	77.0921	117	502	95	below_threshold
Arcobacter ellisii	strain=LMG 26155	GCA_003544915.1	913109	913109	type	True	77.0725	131	502	95	below_threshold
Aliarcobacter faecis	strain=CCUG 66484	GCA_013201705.1	1564138	1564138	type	True	76.9948	122	502	95	below_threshold
[Arcobacter] porcinus	strain=CCUG 56899	GCA_004299785.2	1935204	1935204	type	True	76.9578	124	502	95	below_threshold
Halarcobacter bivalviorum	strain=LMG 26154	GCA_003346815.1	663364	663364	type	True	76.7121	101	502	95	below_threshold
Arcobacter defluvii	strain=LMG 25694	GCA_013201725.1	873191	873191	type	True	76.6927	140	502	95	below_threshold
Arcobacter defluvii	strain=CECT 7697	GCA_004115775.1	873191	873191	type	True	76.6439	146	502	95	below_threshold
Malaciobacter molluscorum	strain=CECT 7696	GCA_003544935.1	1032072	1032072	type	True	76.6357	105	502	95	below_threshold
Poseidonibacter lekithochrous	strain=DSM 100870	GCA_013283835.1	1904463	1904463	type	True	76.5725	93	502	95	below_threshold
Malaciobacter molluscorum	strain=F98-3	GCA_002701265.1	1032072	1032072	type	True	76.5718	106	502	95	below_threshold
Poseidonibacter lekithochrous	strain=LFT 1.7	GCA_001878855.1	1904463	1904463	type	True	76.4572	93	502	95	below_threshold
Halarcobacter ebronensis	strain=LMG 27922	GCA_013201825.1	1462615	1462615	type	True	76.4149	106	502	95	below_threshold
Malaciobacter canalis	strain=F138-33	GCA_002723485.1	1912871	1912871	type	True	76.4125	110	502	95	below_threshold
Malaciobacter canalis	strain=LMG 29148	GCA_008000835.1	1912871	1912871	type	True	76.4023	112	502	95	below_threshold
Halarcobacter ebronensis	strain=CECT 8441	GCA_004116565.1	1462615	1462615	type	True	76.386	102	502	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 10:49:51,117] [INFO] DFAST Taxonomy check result was written to GCA_020718155.1_ASM2071815v1_genomic.fna/tc_result.tsv
[2023-06-29 10:49:51,118] [INFO] ===== Taxonomy check completed =====
[2023-06-29 10:49:51,118] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 10:49:51,118] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d6e57c2-3fc7-45ed-8230-862e4d904045/dqc_reference/checkm_data
[2023-06-29 10:49:51,120] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 10:49:51,144] [INFO] Task started: CheckM
[2023-06-29 10:49:51,145] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020718155.1_ASM2071815v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020718155.1_ASM2071815v1_genomic.fna/checkm_input GCA_020718155.1_ASM2071815v1_genomic.fna/checkm_result
[2023-06-29 10:50:10,117] [INFO] Task succeeded: CheckM
[2023-06-29 10:50:10,119] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 10:50:10,141] [INFO] ===== Completeness check finished =====
[2023-06-29 10:50:10,141] [INFO] ===== Start GTDB Search =====
[2023-06-29 10:50:10,141] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020718155.1_ASM2071815v1_genomic.fna/markers.fasta)
[2023-06-29 10:50:10,142] [INFO] Task started: Blastn
[2023-06-29 10:50:10,142] [INFO] Running command: blastn -query GCA_020718155.1_ASM2071815v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d6e57c2-3fc7-45ed-8230-862e4d904045/dqc_reference/reference_markers_gtdb.fasta -out GCA_020718155.1_ASM2071815v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 10:50:10,954] [INFO] Task succeeded: Blastn
[2023-06-29 10:50:10,981] [INFO] Selected 24 target genomes.
[2023-06-29 10:50:10,981] [INFO] Target genome list was writen to GCA_020718155.1_ASM2071815v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 10:50:11,013] [INFO] Task started: fastANI
[2023-06-29 10:50:11,013] [INFO] Running command: fastANI --query /var/lib/cwl/stgc773fcfe-1905-47c6-b58d-0a978f0df14c/GCA_020718155.1_ASM2071815v1_genomic.fna.gz --refList GCA_020718155.1_ASM2071815v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020718155.1_ASM2071815v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 10:50:20,212] [INFO] Task succeeded: fastANI
[2023-06-29 10:50:20,236] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 10:50:20,237] [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_903821805.1	s__CAIJNA01 sp903821805	81.4846	164	502	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__CAIJNA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013177635.1	s__Aliarcobacter aquimarinus	77.5071	132	502	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013201935.1	s__Aliarcobacter cloacae	77.387	143	502	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.96	95.91	0.93	0.87	3	-
GCF_002993025.1	s__Aliarcobacter cryaerophilus_B	77.3453	120	502	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.88	97.88	0.90	0.90	2	-
GCF_013201625.1	s__Aliarcobacter lanthieri	77.267	113	502	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.15	95.77	0.93	0.89	6	-
GCF_003544815.1	s__Aliarcobacter suis	77.1908	119	502	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003660105.1	s__Aliarcobacter cryaerophilus	77.1631	113	502	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.99	99.99	1.00	0.99	3	-
GCF_900187115.1	s__Aliarcobacter butzleri	77.1586	121	502	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	97.53	96.98	0.89	0.81	50	-
GCA_017995775.1	s__Aliarcobacter sp017995775	77.1	112	502	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.13	99.13	0.84	0.84	2	-
GCF_003544915.1	s__Aliarcobacter ellisii	77.0931	131	502	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.73	97.46	0.92	0.84	3	-
GCA_905479135.1	s__Poseidonibacter sp905479135	77.0201	70	502	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004214815.1	s__Aliarcobacter thereius	77.0009	111	502	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.14	98.62	0.93	0.89	8	-
GCA_004116725.1	s__Malaciobacter sp004116725	76.9767	102	502	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004299785.2	s__Aliarcobacter porcinus	76.9578	124	502	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.76	98.06	0.91	0.88	6	-
GCA_001895145.1	s__Halarcobacter sp001895145	76.95	95	502	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009208075.1	s__Poseidonibacter sp009208075	76.6635	106	502	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	99.63	99.63	0.93	0.93	3	-
GCA_004116465.1	s__Arcobacter sp004116465	76.6489	111	502	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Arcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003252105.1	s__Halarcobacter sp003252105	76.5869	106	502	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013283835.1	s__Poseidonibacter lekithochrous	76.5725	93	502	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	99.16	98.33	0.97	0.93	3	-
GCA_002685075.1	s__Poseidonibacter sp002685075	76.4955	73	502	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018861145.1	s__Poseidonibacter lekithochrous_A	76.4657	109	502	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013201825.1	s__Halarcobacter ebronensis	76.4342	105	502	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	98.25	96.51	0.95	0.90	3	-
GCA_004116495.1	s__Malaciobacter sp004116495	76.3848	106	502	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Malaciobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 10:50:20,239] [INFO] GTDB search result was written to GCA_020718155.1_ASM2071815v1_genomic.fna/result_gtdb.tsv
[2023-06-29 10:50:20,240] [INFO] ===== GTDB Search completed =====
[2023-06-29 10:50:20,249] [INFO] DFAST_QC result json was written to GCA_020718155.1_ASM2071815v1_genomic.fna/dqc_result.json
[2023-06-29 10:50:20,249] [INFO] DFAST_QC completed!
[2023-06-29 10:50:20,249] [INFO] Total running time: 0h0m45s