[2024-01-24 13:31:58,044] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:58,049] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:58,049] [INFO] DQC Reference Directory: /var/lib/cwl/stg34e085bd-71bc-4be5-a454-e35ea2c12939/dqc_reference
[2024-01-24 13:31:59,464] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:59,465] [INFO] Task started: Prodigal
[2024-01-24 13:31:59,465] [INFO] Running command: gunzip -c /var/lib/cwl/stgfab72b21-4b04-4007-9d46-a0a374ea8b5f/GCF_004116335.1_ASM411633v1_genomic.fna.gz | prodigal -d GCF_004116335.1_ASM411633v1_genomic.fna/cds.fna -a GCF_004116335.1_ASM411633v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:05,487] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:05,488] [INFO] Task started: HMMsearch
[2024-01-24 13:32:05,488] [INFO] Running command: hmmsearch --tblout GCF_004116335.1_ASM411633v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34e085bd-71bc-4be5-a454-e35ea2c12939/dqc_reference/reference_markers.hmm GCF_004116335.1_ASM411633v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:05,750] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:05,752] [INFO] Found 6/6 markers.
[2024-01-24 13:32:05,779] [INFO] Query marker FASTA was written to GCF_004116335.1_ASM411633v1_genomic.fna/markers.fasta
[2024-01-24 13:32:05,780] [INFO] Task started: Blastn
[2024-01-24 13:32:05,780] [INFO] Running command: blastn -query GCF_004116335.1_ASM411633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34e085bd-71bc-4be5-a454-e35ea2c12939/dqc_reference/reference_markers.fasta -out GCF_004116335.1_ASM411633v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:06,400] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:06,404] [INFO] Selected 17 target genomes.
[2024-01-24 13:32:06,405] [INFO] Target genome list was writen to GCF_004116335.1_ASM411633v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:06,412] [INFO] Task started: fastANI
[2024-01-24 13:32:06,413] [INFO] Running command: fastANI --query /var/lib/cwl/stgfab72b21-4b04-4007-9d46-a0a374ea8b5f/GCF_004116335.1_ASM411633v1_genomic.fna.gz --refList GCF_004116335.1_ASM411633v1_genomic.fna/target_genomes.txt --output GCF_004116335.1_ASM411633v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:13,682] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:13,683] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34e085bd-71bc-4be5-a454-e35ea2c12939/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:13,683] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34e085bd-71bc-4be5-a454-e35ea2c12939/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:13,697] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:13,697] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:13,698] [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
Candidatus Marinarcus aquaticus	strain=CECT 8987	GCA_004116335.1	2044504	2044504	type	True	100.0	836	836	95	conclusive
Halarcobacter ebronensis	strain=LMG 27922	GCA_013201825.1	1462615	1462615	type	True	78.4953	213	836	95	below_threshold
Malaciobacter pacificus	strain=LMG 26638	GCA_004214795.1	1080223	1080223	type	True	78.4915	165	836	95	below_threshold
Halarcobacter ebronensis	strain=CECT 8441	GCA_004116565.1	1462615	1462615	type	True	78.4911	205	836	95	below_threshold
[Halarcobacter] arenosus	strain=CAU 1517	GCA_005771535.1	2576037	2576037	type	True	78.4427	192	836	95	below_threshold
Halarcobacter bivalviorum	strain=CECT 7835	GCA_004116675.1	663364	663364	type	True	78.1033	213	836	95	below_threshold
Poseidonibacter lekithochrous	strain=DSM 100870	GCA_013283835.1	1904463	1904463	type	True	78.0327	142	836	95	below_threshold
Halarcobacter bivalviorum	strain=LMG 26154	GCA_003346815.1	663364	663364	type	True	78.0117	215	836	95	below_threshold
Arcobacter suis	strain=CECT7833	GCA_004023465.1	1278212	1278212	type	True	77.9871	141	836	95	below_threshold
Arcobacter suis	strain=CECT 7833	GCA_003544815.1	1278212	1278212	type	True	77.8594	149	836	95	below_threshold
Halarcobacter anaerophilus	strain=DSM 24636	GCA_006459125.1	877500	877500	type	True	77.8442	160	836	95	below_threshold
Halarcobacter anaerophilus	strain=DSM 24636	GCA_004116345.1	877500	877500	type	True	77.789	163	836	95	below_threshold
Arcobacter ellisii	strain=CECT 7837	GCA_004115815.1	913109	913109	type	True	77.6779	150	836	95	below_threshold
Arcobacter ellisii	strain=LMG 26155	GCA_003544915.1	913109	913109	type	True	77.639	158	836	95	below_threshold
Aliarcobacter trophiarum	strain=LMG 25534	GCA_003355515.1	708186	708186	type	True	77.2047	109	836	95	below_threshold
Aliarcobacter trophiarum	strain=LMG 25534	GCA_004116585.1	708186	708186	type	True	77.1976	107	836	95	below_threshold
Aliarcobacter trophiarum	strain=LMG 25534	GCA_024584015.1	708186	708186	type	True	77.1279	104	836	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:13,700] [INFO] DFAST Taxonomy check result was written to GCF_004116335.1_ASM411633v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:13,700] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:13,700] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:13,701] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34e085bd-71bc-4be5-a454-e35ea2c12939/dqc_reference/checkm_data
[2024-01-24 13:32:13,702] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:13,734] [INFO] Task started: CheckM
[2024-01-24 13:32:13,734] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004116335.1_ASM411633v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004116335.1_ASM411633v1_genomic.fna/checkm_input GCF_004116335.1_ASM411633v1_genomic.fna/checkm_result
[2024-01-24 13:32:38,843] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:38,843] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:38,859] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:38,859] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:38,859] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004116335.1_ASM411633v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:38,860] [INFO] Task started: Blastn
[2024-01-24 13:32:38,860] [INFO] Running command: blastn -query GCF_004116335.1_ASM411633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34e085bd-71bc-4be5-a454-e35ea2c12939/dqc_reference/reference_markers_gtdb.fasta -out GCF_004116335.1_ASM411633v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:39,774] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:39,779] [INFO] Selected 16 target genomes.
[2024-01-24 13:32:39,779] [INFO] Target genome list was writen to GCF_004116335.1_ASM411633v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:39,794] [INFO] Task started: fastANI
[2024-01-24 13:32:39,795] [INFO] Running command: fastANI --query /var/lib/cwl/stgfab72b21-4b04-4007-9d46-a0a374ea8b5f/GCF_004116335.1_ASM411633v1_genomic.fna.gz --refList GCF_004116335.1_ASM411633v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004116335.1_ASM411633v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:32:47,569] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:47,583] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:32:47,583] [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_004116335.1	s__UBA4036 sp004116335	100.0	836	836	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__UBA4036	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002382325.1	s__UBA4036 sp002382325	79.0738	349	836	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__UBA4036	95.0	100.00	100.00	1.00	1.00	6	-
GCA_004118855.1	s__Halarcobacter sp004118855	79.0219	195	836	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373175.1	s__Halarcobacter sp013373175	78.6315	197	836	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004214795.1	s__Aliarcobacter pacificus	78.5016	166	836	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_013201825.1	s__Halarcobacter ebronensis	78.4839	214	836	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	98.25	96.51	0.95	0.90	3	-
GCF_005771535.1	s__Halarcobacter arenosus	78.4427	192	836	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001895145.1	s__Halarcobacter sp001895145	78.0777	181	836	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003346815.1	s__Halarcobacter bivalviorum	78.0287	214	836	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Halarcobacter	95.0	98.23	96.46	0.96	0.92	3	-
GCA_003252105.1	s__Halarcobacter sp003252105	78.0272	192	836	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	78.0182	144	836	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Poseidonibacter	95.0	99.16	98.33	0.97	0.93	3	-
GCA_001655195.1	s__Arcobacter_A sp001655195	77.9658	234	836	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Arcobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003544915.1	s__Aliarcobacter ellisii	77.62	159	836	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	98.73	97.46	0.92	0.84	3	-
GCA_018816105.1	s__Aliarcobacter sp018816105	77.3032	141	836	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003355515.1	s__Aliarcobacter trophiarum	77.2047	109	836	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__Aliarcobacter	95.0	99.76	99.53	0.96	0.92	3	-
GCA_018662405.1	s__JADHTT01 sp018662405	76.9842	55	836	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Arcobacteraceae;g__JADHTT01	95.0	99.77	99.69	0.93	0.90	13	-
--------------------------------------------------------------------------------
[2024-01-24 13:32:47,585] [INFO] GTDB search result was written to GCF_004116335.1_ASM411633v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:32:47,585] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:32:47,590] [INFO] DFAST_QC result json was written to GCF_004116335.1_ASM411633v1_genomic.fna/dqc_result.json
[2024-01-24 13:32:47,590] [INFO] DFAST_QC completed!
[2024-01-24 13:32:47,590] [INFO] Total running time: 0h0m50s