[2024-01-24 11:09:50,716] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:09:50,719] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:09:50,719] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d191d5d-62a4-4e21-8957-9b50313e44d4/dqc_reference
[2024-01-24 11:09:53,302] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:09:53,303] [INFO] Task started: Prodigal
[2024-01-24 11:09:53,304] [INFO] Running command: gunzip -c /var/lib/cwl/stg51dc8ca0-533b-4102-a223-bde662300059/GCF_001723285.1_ASM172328v1_genomic.fna.gz | prodigal -d GCF_001723285.1_ASM172328v1_genomic.fna/cds.fna -a GCF_001723285.1_ASM172328v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:10:02,759] [INFO] Task succeeded: Prodigal
[2024-01-24 11:10:02,760] [INFO] Task started: HMMsearch
[2024-01-24 11:10:02,760] [INFO] Running command: hmmsearch --tblout GCF_001723285.1_ASM172328v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d191d5d-62a4-4e21-8957-9b50313e44d4/dqc_reference/reference_markers.hmm GCF_001723285.1_ASM172328v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:10:02,997] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:10:02,998] [INFO] Found 6/6 markers.
[2024-01-24 11:10:03,025] [INFO] Query marker FASTA was written to GCF_001723285.1_ASM172328v1_genomic.fna/markers.fasta
[2024-01-24 11:10:03,025] [INFO] Task started: Blastn
[2024-01-24 11:10:03,025] [INFO] Running command: blastn -query GCF_001723285.1_ASM172328v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d191d5d-62a4-4e21-8957-9b50313e44d4/dqc_reference/reference_markers.fasta -out GCF_001723285.1_ASM172328v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:10:03,912] [INFO] Task succeeded: Blastn
[2024-01-24 11:10:03,916] [INFO] Selected 17 target genomes.
[2024-01-24 11:10:03,917] [INFO] Target genome list was writen to GCF_001723285.1_ASM172328v1_genomic.fna/target_genomes.txt
[2024-01-24 11:10:03,941] [INFO] Task started: fastANI
[2024-01-24 11:10:03,941] [INFO] Running command: fastANI --query /var/lib/cwl/stg51dc8ca0-533b-4102-a223-bde662300059/GCF_001723285.1_ASM172328v1_genomic.fna.gz --refList GCF_001723285.1_ASM172328v1_genomic.fna/target_genomes.txt --output GCF_001723285.1_ASM172328v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:10:17,024] [INFO] Task succeeded: fastANI
[2024-01-24 11:10:17,025] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d191d5d-62a4-4e21-8957-9b50313e44d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:10:17,025] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d191d5d-62a4-4e21-8957-9b50313e44d4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:10:17,042] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:10:17,042] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:10:17,042] [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
Methyloceanibacter methanicus	strain=R-67174	GCA_001723285.1	1774968	1774968	type	True	100.0	1040	1040	95	conclusive
Methyloceanibacter stevinii	strain=R-67176	GCA_001723355.1	1774970	1774970	type	True	83.3074	798	1040	95	below_threshold
Methyloceanibacter caenitepidi	strain=Gela4	GCA_000828475.1	1384459	1384459	type	True	82.9727	756	1040	95	below_threshold
Methyloceanibacter marginalis	strain=R-67177	GCA_001723295.1	1774971	1774971	type	True	79.7015	389	1040	95	below_threshold
Methyloceanibacter superfactus	strain=R-67175	GCA_001723305.1	1774969	1774969	type	True	79.3891	506	1040	95	below_threshold
Methyloligella halotolerans	strain=VKM B-2706	GCA_001708935.1	1177755	1177755	type	True	77.9062	274	1040	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	77.2333	163	1040	95	below_threshold
Hyphomicrobium album	strain=XQ2	GCA_009708035.1	2665159	2665159	type	True	77.2199	152	1040	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	77.0298	110	1040	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	77.0298	110	1040	95	below_threshold
Ancylobacter sonchi	strain=VKM B-3145	GCA_018390695.1	1937790	1937790	type	True	76.7165	160	1040	95	below_threshold
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	76.7061	127	1040	95	below_threshold
Erythrobacter colymbi	strain=JCM 18338	GCA_002155685.1	1161202	1161202	type	True	76.7028	57	1040	95	below_threshold
Rhodomicrobium udaipurense	strain=JA643	GCA_000636015.1	1202716	1202716	type	True	76.5295	111	1040	95	below_threshold
Sinorhizobium arboris	strain=LMG 14919	GCA_000427465.1	76745	76745	type	True	76.4324	121	1040	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	76.3859	159	1040	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	75.9509	124	1040	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:10:17,044] [INFO] DFAST Taxonomy check result was written to GCF_001723285.1_ASM172328v1_genomic.fna/tc_result.tsv
[2024-01-24 11:10:17,045] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:10:17,045] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:10:17,045] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d191d5d-62a4-4e21-8957-9b50313e44d4/dqc_reference/checkm_data
[2024-01-24 11:10:17,046] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:10:17,076] [INFO] Task started: CheckM
[2024-01-24 11:10:17,076] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001723285.1_ASM172328v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001723285.1_ASM172328v1_genomic.fna/checkm_input GCF_001723285.1_ASM172328v1_genomic.fna/checkm_result
[2024-01-24 11:10:47,558] [INFO] Task succeeded: CheckM
[2024-01-24 11:10:47,558] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:10:47,577] [INFO] ===== Completeness check finished =====
[2024-01-24 11:10:47,577] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:10:47,577] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001723285.1_ASM172328v1_genomic.fna/markers.fasta)
[2024-01-24 11:10:47,578] [INFO] Task started: Blastn
[2024-01-24 11:10:47,578] [INFO] Running command: blastn -query GCF_001723285.1_ASM172328v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d191d5d-62a4-4e21-8957-9b50313e44d4/dqc_reference/reference_markers_gtdb.fasta -out GCF_001723285.1_ASM172328v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:10:49,240] [INFO] Task succeeded: Blastn
[2024-01-24 11:10:49,244] [INFO] Selected 9 target genomes.
[2024-01-24 11:10:49,244] [INFO] Target genome list was writen to GCF_001723285.1_ASM172328v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:10:49,251] [INFO] Task started: fastANI
[2024-01-24 11:10:49,251] [INFO] Running command: fastANI --query /var/lib/cwl/stg51dc8ca0-533b-4102-a223-bde662300059/GCF_001723285.1_ASM172328v1_genomic.fna.gz --refList GCF_001723285.1_ASM172328v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001723285.1_ASM172328v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:10:57,263] [INFO] Task succeeded: fastANI
[2024-01-24 11:10:57,276] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:10:57,276] [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_001723285.1	s__Methyloceanibacter methanicus	100.0	1040	1040	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003071365.1	s__Methyloceanibacter sp003071365	83.395	778	1040	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001723355.1	s__Methyloceanibacter stevinii	83.3074	798	1040	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000828475.1	s__Methyloceanibacter caenitepidi	82.9727	756	1040	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002482645.1	s__Methyloceanibacter sp002482645	81.8962	693	1040	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter	95.0	98.85	98.85	0.80	0.80	2	-
GCF_001579845.1	s__Z2-YC6860 sp001579845	77.0635	138	1040	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Z2-YC6860	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905339215.1	s__DUSC01 sp008933895	77.0021	119	1040	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__DUSC01	95.0	99.82	99.82	0.93	0.93	2	-
GCA_019245415.1	s__Rhizomicrobium sp019245415	76.952	107	1040	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Micropepsales;f__Micropepsaceae;g__Rhizomicrobium	95.0	99.94	99.94	0.99	0.99	2	-
GCF_018069605.1	s__Microvirga sp018069605	76.5374	127	1040	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:10:57,278] [INFO] GTDB search result was written to GCF_001723285.1_ASM172328v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:10:57,278] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:10:57,281] [INFO] DFAST_QC result json was written to GCF_001723285.1_ASM172328v1_genomic.fna/dqc_result.json
[2024-01-24 11:10:57,281] [INFO] DFAST_QC completed!
[2024-01-24 11:10:57,282] [INFO] Total running time: 0h1m7s