[2024-01-25 20:14:50,598] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:14:50,599] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:14:50,599] [INFO] DQC Reference Directory: /var/lib/cwl/stgb7913492-a7f4-48ce-b09a-3b314a0deb55/dqc_reference
[2024-01-25 20:14:51,746] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:14:51,746] [INFO] Task started: Prodigal
[2024-01-25 20:14:51,747] [INFO] Running command: gunzip -c /var/lib/cwl/stg78ff5753-658c-4746-b84a-b4c3ab68c003/GCF_027571405.1_ASM2757140v1_genomic.fna.gz | prodigal -d GCF_027571405.1_ASM2757140v1_genomic.fna/cds.fna -a GCF_027571405.1_ASM2757140v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:15:02,901] [INFO] Task succeeded: Prodigal
[2024-01-25 20:15:02,902] [INFO] Task started: HMMsearch
[2024-01-25 20:15:02,902] [INFO] Running command: hmmsearch --tblout GCF_027571405.1_ASM2757140v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb7913492-a7f4-48ce-b09a-3b314a0deb55/dqc_reference/reference_markers.hmm GCF_027571405.1_ASM2757140v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:15:03,118] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:15:03,119] [INFO] Found 6/6 markers.
[2024-01-25 20:15:03,156] [INFO] Query marker FASTA was written to GCF_027571405.1_ASM2757140v1_genomic.fna/markers.fasta
[2024-01-25 20:15:03,157] [INFO] Task started: Blastn
[2024-01-25 20:15:03,157] [INFO] Running command: blastn -query GCF_027571405.1_ASM2757140v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7913492-a7f4-48ce-b09a-3b314a0deb55/dqc_reference/reference_markers.fasta -out GCF_027571405.1_ASM2757140v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:04,040] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:04,044] [INFO] Selected 15 target genomes.
[2024-01-25 20:15:04,044] [INFO] Target genome list was writen to GCF_027571405.1_ASM2757140v1_genomic.fna/target_genomes.txt
[2024-01-25 20:15:04,062] [INFO] Task started: fastANI
[2024-01-25 20:15:04,062] [INFO] Running command: fastANI --query /var/lib/cwl/stg78ff5753-658c-4746-b84a-b4c3ab68c003/GCF_027571405.1_ASM2757140v1_genomic.fna.gz --refList GCF_027571405.1_ASM2757140v1_genomic.fna/target_genomes.txt --output GCF_027571405.1_ASM2757140v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:15:17,776] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:17,776] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb7913492-a7f4-48ce-b09a-3b314a0deb55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:15:17,776] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb7913492-a7f4-48ce-b09a-3b314a0deb55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:15:17,786] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:15:17,786] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:15:17,787] [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
Methylocystis parvus	strain=OBBP	GCA_000283235.1	134	134	type	True	99.9501	1441	1508	95	conclusive
Methylocystis silviterrae	strain=FS	GCA_013350005.1	2743612	2743612	type	True	79.8375	623	1508	95	below_threshold
Methylocystis hirsuta	strain=CSC1	GCA_003722355.1	369798	369798	type	True	79.7356	642	1508	95	below_threshold
Methylocystis rosea	strain=SV97	GCA_000372845.1	173366	173366	type	True	79.681	611	1508	95	below_threshold
Methylosinus sporium	strain=DSM 17706	GCA_009811675.1	428	428	type	True	79.3287	577	1508	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_000178815.2	426	426	type	True	79.2933	590	1508	95	below_threshold
Methylosinus sporium	strain=DSM 17706	GCA_003113265.1	428	428	type	True	79.2214	549	1508	95	below_threshold
Methylosinus trichosporium	strain=OB3b	GCA_002752655.1	426	426	type	True	79.2062	594	1508	95	below_threshold
Methylorubrum aminovorans	strain=NBRC 15686	GCA_022179725.1	269069	269069	type	True	77.0903	262	1508	95	below_threshold
Bradyrhizobium aeschynomenes	strain=83002	GCA_013178945.1	2734909	2734909	type	True	77.0715	270	1508	95	below_threshold
Methylobacterium marchantiae	strain=DSM 21328	GCA_022179405.1	600331	600331	type	True	77.0182	216	1508	95	below_threshold
Kaistia granuli	strain=Ko04	GCA_000380505.1	363259	363259	type	True	76.9733	221	1508	95	below_threshold
Bradyrhizobium betae	strain=CECT 5829	GCA_024806875.1	244734	244734	type	True	76.909	254	1508	95	below_threshold
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	76.8802	263	1508	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	76.6565	271	1508	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:15:17,788] [INFO] DFAST Taxonomy check result was written to GCF_027571405.1_ASM2757140v1_genomic.fna/tc_result.tsv
[2024-01-25 20:15:17,789] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:15:17,789] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:15:17,789] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb7913492-a7f4-48ce-b09a-3b314a0deb55/dqc_reference/checkm_data
[2024-01-25 20:15:17,790] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:15:17,834] [INFO] Task started: CheckM
[2024-01-25 20:15:17,834] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027571405.1_ASM2757140v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027571405.1_ASM2757140v1_genomic.fna/checkm_input GCF_027571405.1_ASM2757140v1_genomic.fna/checkm_result
[2024-01-25 20:15:51,955] [INFO] Task succeeded: CheckM
[2024-01-25 20:15:51,956] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:15:51,974] [INFO] ===== Completeness check finished =====
[2024-01-25 20:15:51,974] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:15:51,975] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027571405.1_ASM2757140v1_genomic.fna/markers.fasta)
[2024-01-25 20:15:51,975] [INFO] Task started: Blastn
[2024-01-25 20:15:51,975] [INFO] Running command: blastn -query GCF_027571405.1_ASM2757140v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7913492-a7f4-48ce-b09a-3b314a0deb55/dqc_reference/reference_markers_gtdb.fasta -out GCF_027571405.1_ASM2757140v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:53,597] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:53,600] [INFO] Selected 8 target genomes.
[2024-01-25 20:15:53,600] [INFO] Target genome list was writen to GCF_027571405.1_ASM2757140v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:15:53,983] [INFO] Task started: fastANI
[2024-01-25 20:15:53,984] [INFO] Running command: fastANI --query /var/lib/cwl/stg78ff5753-658c-4746-b84a-b4c3ab68c003/GCF_027571405.1_ASM2757140v1_genomic.fna.gz --refList GCF_027571405.1_ASM2757140v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027571405.1_ASM2757140v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:16:02,408] [INFO] Task succeeded: fastANI
[2024-01-25 20:16:02,415] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:16:02,415] [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_000283235.1	s__Methylocystis parvus	99.9501	1441	1508	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_016745395.1	s__Methylocystis sp016745395	82.7335	841	1508	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011058845.1	s__Methylocystis sp011058845	82.5145	832	1508	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002929055.1	s__Methylocystis sp002929055	82.3182	720	1508	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963405.1	s__Methylocystis sp003963405	82.2172	779	1508	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000188155.2	s__Methylocystis sp000188155	82.1119	795	1508	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869555.1	s__Methylocystis sp016869555	80.0151	588	1508	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	99.54	99.54	0.92	0.92	2	-
GCF_002752655.1	s__Methylosinus trichosporium	79.2424	592	1508	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylosinus	95.0	99.98	99.98	1.00	1.00	3	-
--------------------------------------------------------------------------------
[2024-01-25 20:16:02,417] [INFO] GTDB search result was written to GCF_027571405.1_ASM2757140v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:16:02,417] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:16:02,422] [INFO] DFAST_QC result json was written to GCF_027571405.1_ASM2757140v1_genomic.fna/dqc_result.json
[2024-01-25 20:16:02,423] [INFO] DFAST_QC completed!
[2024-01-25 20:16:02,423] [INFO] Total running time: 0h1m12s