[2024-01-25 19:37:05,779] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:37:05,780] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:37:05,780] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf4eb343-8728-4de4-b9eb-82877bbdd2b4/dqc_reference
[2024-01-25 19:37:07,004] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:37:07,005] [INFO] Task started: Prodigal
[2024-01-25 19:37:07,005] [INFO] Running command: gunzip -c /var/lib/cwl/stge5617c30-dc1c-4622-9897-c2dd787d8abe/GCF_000421465.1_ASM42146v1_genomic.fna.gz | prodigal -d GCF_000421465.1_ASM42146v1_genomic.fna/cds.fna -a GCF_000421465.1_ASM42146v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:37:16,658] [INFO] Task succeeded: Prodigal
[2024-01-25 19:37:16,658] [INFO] Task started: HMMsearch
[2024-01-25 19:37:16,658] [INFO] Running command: hmmsearch --tblout GCF_000421465.1_ASM42146v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf4eb343-8728-4de4-b9eb-82877bbdd2b4/dqc_reference/reference_markers.hmm GCF_000421465.1_ASM42146v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:37:16,927] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:37:16,929] [INFO] Found 6/6 markers.
[2024-01-25 19:37:16,961] [INFO] Query marker FASTA was written to GCF_000421465.1_ASM42146v1_genomic.fna/markers.fasta
[2024-01-25 19:37:16,961] [INFO] Task started: Blastn
[2024-01-25 19:37:16,961] [INFO] Running command: blastn -query GCF_000421465.1_ASM42146v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf4eb343-8728-4de4-b9eb-82877bbdd2b4/dqc_reference/reference_markers.fasta -out GCF_000421465.1_ASM42146v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:37:17,574] [INFO] Task succeeded: Blastn
[2024-01-25 19:37:17,577] [INFO] Selected 23 target genomes.
[2024-01-25 19:37:17,577] [INFO] Target genome list was writen to GCF_000421465.1_ASM42146v1_genomic.fna/target_genomes.txt
[2024-01-25 19:37:17,602] [INFO] Task started: fastANI
[2024-01-25 19:37:17,603] [INFO] Running command: fastANI --query /var/lib/cwl/stge5617c30-dc1c-4622-9897-c2dd787d8abe/GCF_000421465.1_ASM42146v1_genomic.fna.gz --refList GCF_000421465.1_ASM42146v1_genomic.fna/target_genomes.txt --output GCF_000421465.1_ASM42146v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:37:32,175] [INFO] Task succeeded: fastANI
[2024-01-25 19:37:32,176] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf4eb343-8728-4de4-b9eb-82877bbdd2b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:37:32,176] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf4eb343-8728-4de4-b9eb-82877bbdd2b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:37:32,186] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:37:32,186] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:37:32,186] [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
Methylohalobius crimeensis	strain=10Ki	GCA_000421465.1	244365	244365	type	True	100.0	1166	1168	95	conclusive
Methylococcus capsulatus	strain=ATCC 19069	GCA_000424685.1	414	414	type	True	76.9542	90	1168	95	below_threshold
Methylococcus geothermalis	strain=IM1	GCA_012769535.1	2681310	2681310	type	True	76.9535	93	1168	95	below_threshold
Methylogaea oryzae	strain=E10	GCA_019669985.1	1295382	1295382	type	True	76.8489	116	1168	95	below_threshold
Sulfurivermis fontis	strain=JG42	GCA_004001245.1	1972068	1972068	type	True	76.6495	68	1168	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	76.5739	72	1168	95	below_threshold
Methylocaldum marinum	strain=S8	GCA_003584645.1	1432792	1432792	type	True	76.5406	74	1168	95	below_threshold
Thioalkalivibrio denitrificans	strain=ALJD	GCA_002000365.1	108003	108003	type	True	76.4406	57	1168	95	below_threshold
Arhodomonas aquaeolei	strain=DSM 8974	GCA_000374645.1	2369	2369	type	True	76.4313	52	1168	95	below_threshold
Methyloterricola oryzae	strain=73a	GCA_000934725.1	1495050	1495050	type	True	76.4293	93	1168	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	76.3832	82	1168	95	below_threshold
Methylococcus capsulatus	strain=Texas	GCA_000297615.1	414	414	type	True	76.3091	82	1168	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	75.9759	50	1168	95	below_threshold
Azoarcus nasutitermitis	strain=CC-YHH838	GCA_004801295.1	2565930	2565930	type	True	75.9334	52	1168	95	below_threshold
Allochromatium humboldtianum	strain=DSM 21881	GCA_013385175.1	504901	504901	type	True	75.8742	59	1168	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:37:32,188] [INFO] DFAST Taxonomy check result was written to GCF_000421465.1_ASM42146v1_genomic.fna/tc_result.tsv
[2024-01-25 19:37:32,189] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:37:32,189] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:37:32,189] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf4eb343-8728-4de4-b9eb-82877bbdd2b4/dqc_reference/checkm_data
[2024-01-25 19:37:32,190] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:37:32,226] [INFO] Task started: CheckM
[2024-01-25 19:37:32,227] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000421465.1_ASM42146v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000421465.1_ASM42146v1_genomic.fna/checkm_input GCF_000421465.1_ASM42146v1_genomic.fna/checkm_result
[2024-01-25 19:38:02,337] [INFO] Task succeeded: CheckM
[2024-01-25 19:38:02,338] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:38:02,361] [INFO] ===== Completeness check finished =====
[2024-01-25 19:38:02,361] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:38:02,362] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000421465.1_ASM42146v1_genomic.fna/markers.fasta)
[2024-01-25 19:38:02,362] [INFO] Task started: Blastn
[2024-01-25 19:38:02,362] [INFO] Running command: blastn -query GCF_000421465.1_ASM42146v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf4eb343-8728-4de4-b9eb-82877bbdd2b4/dqc_reference/reference_markers_gtdb.fasta -out GCF_000421465.1_ASM42146v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:38:03,301] [INFO] Task succeeded: Blastn
[2024-01-25 19:38:03,304] [INFO] Selected 24 target genomes.
[2024-01-25 19:38:03,305] [INFO] Target genome list was writen to GCF_000421465.1_ASM42146v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:38:03,343] [INFO] Task started: fastANI
[2024-01-25 19:38:03,344] [INFO] Running command: fastANI --query /var/lib/cwl/stge5617c30-dc1c-4622-9897-c2dd787d8abe/GCF_000421465.1_ASM42146v1_genomic.fna.gz --refList GCF_000421465.1_ASM42146v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000421465.1_ASM42146v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:38:18,716] [INFO] Task succeeded: fastANI
[2024-01-25 19:38:18,724] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:38:18,724] [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_000421465.1	s__Methylohalobius crimeensis	100.0	1165	1168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylothermaceae;g__Methylohalobius	95.0	95.22	95.22	0.89	0.89	2	conclusive
GCF_012769535.1	s__Methylococcus sp012769535	77.0714	94	1168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001566965.1	s__Methylohalobius sp001566965	76.9572	128	1168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylothermaceae;g__Methylohalobius	95.0	99.98	99.98	0.97	0.97	2	-
GCF_016106025.1	s__Methylococcus sp016106025	76.6516	85	1168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584645.1	s__Methylocaldum marinum	76.5652	75	1168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylocaldum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051655.1	s__DRKS01 sp011051655	76.4596	52	1168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__DRKS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337735.1	s__Thioalbus denitrificans	76.3832	82	1168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-26407;f__DSM-26407;g__Thioalbus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374645.1	s__Arhodomonas aquaeolei	76.3727	50	1168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Nitrococcaceae;g__Arhodomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018435665.1	s__M0108 sp018435665	75.9631	62	1168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__M0108	95.0	99.16	99.16	0.79	0.79	2	-
GCF_004341245.1	s__Plasticicumulans_A lactativorans	75.9478	51	1168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004299145.1	s__Methylogaea sp004299145	75.7751	70	1168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylococcaceae;g__Methylogaea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:38:18,725] [INFO] GTDB search result was written to GCF_000421465.1_ASM42146v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:38:18,726] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:38:18,729] [INFO] DFAST_QC result json was written to GCF_000421465.1_ASM42146v1_genomic.fna/dqc_result.json
[2024-01-25 19:38:18,729] [INFO] DFAST_QC completed!
[2024-01-25 19:38:18,729] [INFO] Total running time: 0h1m13s