[2023-06-13 02:48:20,283] [INFO] DFAST_QC pipeline started.
[2023-06-13 02:48:20,285] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 02:48:20,285] [INFO] DQC Reference Directory: /var/lib/cwl/stg53fdd622-7e88-4127-85f2-ffdc6880034e/dqc_reference
[2023-06-13 02:48:21,472] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 02:48:21,472] [INFO] Task started: Prodigal
[2023-06-13 02:48:21,473] [INFO] Running command: gunzip -c /var/lib/cwl/stgdef74f1d-426e-40f6-9e65-c2a32b0c5489/GCA_938009595.1_N2_Bin_METABAT_118_1_genomic.fna.gz | prodigal -d GCA_938009595.1_N2_Bin_METABAT_118_1_genomic.fna/cds.fna -a GCA_938009595.1_N2_Bin_METABAT_118_1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 02:48:26,671] [INFO] Task succeeded: Prodigal
[2023-06-13 02:48:26,672] [INFO] Task started: HMMsearch
[2023-06-13 02:48:26,672] [INFO] Running command: hmmsearch --tblout GCA_938009595.1_N2_Bin_METABAT_118_1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg53fdd622-7e88-4127-85f2-ffdc6880034e/dqc_reference/reference_markers.hmm GCA_938009595.1_N2_Bin_METABAT_118_1_genomic.fna/protein.faa > /dev/null
[2023-06-13 02:48:26,899] [INFO] Task succeeded: HMMsearch
[2023-06-13 02:48:26,901] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgdef74f1d-426e-40f6-9e65-c2a32b0c5489/GCA_938009595.1_N2_Bin_METABAT_118_1_genomic.fna.gz]
[2023-06-13 02:48:26,928] [INFO] Query marker FASTA was written to GCA_938009595.1_N2_Bin_METABAT_118_1_genomic.fna/markers.fasta
[2023-06-13 02:48:26,929] [INFO] Task started: Blastn
[2023-06-13 02:48:26,929] [INFO] Running command: blastn -query GCA_938009595.1_N2_Bin_METABAT_118_1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53fdd622-7e88-4127-85f2-ffdc6880034e/dqc_reference/reference_markers.fasta -out GCA_938009595.1_N2_Bin_METABAT_118_1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 02:48:27,537] [INFO] Task succeeded: Blastn
[2023-06-13 02:48:27,542] [INFO] Selected 12 target genomes.
[2023-06-13 02:48:27,542] [INFO] Target genome list was writen to GCA_938009595.1_N2_Bin_METABAT_118_1_genomic.fna/target_genomes.txt
[2023-06-13 02:48:27,544] [INFO] Task started: fastANI
[2023-06-13 02:48:27,545] [INFO] Running command: fastANI --query /var/lib/cwl/stgdef74f1d-426e-40f6-9e65-c2a32b0c5489/GCA_938009595.1_N2_Bin_METABAT_118_1_genomic.fna.gz --refList GCA_938009595.1_N2_Bin_METABAT_118_1_genomic.fna/target_genomes.txt --output GCA_938009595.1_N2_Bin_METABAT_118_1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 02:48:35,912] [INFO] Task succeeded: fastANI
[2023-06-13 02:48:35,913] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg53fdd622-7e88-4127-85f2-ffdc6880034e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 02:48:35,913] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg53fdd622-7e88-4127-85f2-ffdc6880034e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 02:48:35,931] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 02:48:35,931] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 02:48:35,931] [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 marginalis	strain=R-67177	GCA_001723295.1	1774971	1774971	type	True	80.7872	306	543	95	below_threshold
Methyloceanibacter superfactus	strain=R-67175	GCA_001723305.1	1774969	1774969	type	True	80.5221	398	543	95	below_threshold
Methyloceanibacter stevinii	strain=R-67176	GCA_001723355.1	1774970	1774970	type	True	78.8525	304	543	95	below_threshold
Methyloceanibacter methanicus	strain=R-67174	GCA_001723285.1	1774968	1774968	type	True	78.8212	301	543	95	below_threshold
Methyloceanibacter caenitepidi	strain=Gela4	GCA_000828475.1	1384459	1384459	type	True	78.7682	278	543	95	below_threshold
Methyloligella halotolerans	strain=VKM B-2706	GCA_001708935.1	1177755	1177755	type	True	77.4042	158	543	95	below_threshold
Dichotomicrobium thermohalophilum	strain=DSM 5002	GCA_003550175.1	933063	933063	type	True	76.5425	61	543	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	76.3841	74	543	95	below_threshold
Bradyrhizobium aeschynomenes	strain=83002	GCA_013178945.1	2734909	2734909	type	True	76.33	92	543	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	76.2042	70	543	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	75.6738	57	543	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 02:48:35,933] [INFO] DFAST Taxonomy check result was written to GCA_938009595.1_N2_Bin_METABAT_118_1_genomic.fna/tc_result.tsv
[2023-06-13 02:48:35,934] [INFO] ===== Taxonomy check completed =====
[2023-06-13 02:48:35,934] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 02:48:35,934] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg53fdd622-7e88-4127-85f2-ffdc6880034e/dqc_reference/checkm_data
[2023-06-13 02:48:35,936] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 02:48:35,962] [INFO] Task started: CheckM
[2023-06-13 02:48:35,962] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938009595.1_N2_Bin_METABAT_118_1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938009595.1_N2_Bin_METABAT_118_1_genomic.fna/checkm_input GCA_938009595.1_N2_Bin_METABAT_118_1_genomic.fna/checkm_result
[2023-06-13 02:48:57,785] [INFO] Task succeeded: CheckM
[2023-06-13 02:48:57,786] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 02:48:57,813] [INFO] ===== Completeness check finished =====
[2023-06-13 02:48:57,814] [INFO] ===== Start GTDB Search =====
[2023-06-13 02:48:57,814] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938009595.1_N2_Bin_METABAT_118_1_genomic.fna/markers.fasta)
[2023-06-13 02:48:57,815] [INFO] Task started: Blastn
[2023-06-13 02:48:57,815] [INFO] Running command: blastn -query GCA_938009595.1_N2_Bin_METABAT_118_1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53fdd622-7e88-4127-85f2-ffdc6880034e/dqc_reference/reference_markers_gtdb.fasta -out GCA_938009595.1_N2_Bin_METABAT_118_1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 02:48:58,577] [INFO] Task succeeded: Blastn
[2023-06-13 02:48:58,582] [INFO] Selected 10 target genomes.
[2023-06-13 02:48:58,583] [INFO] Target genome list was writen to GCA_938009595.1_N2_Bin_METABAT_118_1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 02:48:58,586] [INFO] Task started: fastANI
[2023-06-13 02:48:58,586] [INFO] Running command: fastANI --query /var/lib/cwl/stgdef74f1d-426e-40f6-9e65-c2a32b0c5489/GCA_938009595.1_N2_Bin_METABAT_118_1_genomic.fna.gz --refList GCA_938009595.1_N2_Bin_METABAT_118_1_genomic.fna/target_genomes_gtdb.txt --output GCA_938009595.1_N2_Bin_METABAT_118_1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 02:49:03,559] [INFO] Task succeeded: fastANI
[2023-06-13 02:49:03,576] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 02:49:03,577] [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_002390155.1	s__Methyloceanibacter sp002390155	98.7188	261	543	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_001723295.1	s__Methyloceanibacter marginalis	80.7472	308	543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001723305.1	s__Methyloceanibacter superfactus	80.5221	398	543	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	78.8525	304	543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003071365.1	s__Methyloceanibacter sp003071365	78.8504	289	543	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	78.844	309	543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter	95.0	98.85	98.85	0.80	0.80	2	-
GCF_001723285.1	s__Methyloceanibacter methanicus	78.8212	301	543	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	78.7829	277	543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018067145.1	s__Methyloceanibacter sp018067145	78.5601	283	543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869535.1	s__Methyloceanibacter sp016869535	78.2611	208	543	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Methyloligellaceae;g__Methyloceanibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 02:49:03,579] [INFO] GTDB search result was written to GCA_938009595.1_N2_Bin_METABAT_118_1_genomic.fna/result_gtdb.tsv
[2023-06-13 02:49:03,579] [INFO] ===== GTDB Search completed =====
[2023-06-13 02:49:03,583] [INFO] DFAST_QC result json was written to GCA_938009595.1_N2_Bin_METABAT_118_1_genomic.fna/dqc_result.json
[2023-06-13 02:49:03,584] [INFO] DFAST_QC completed!
[2023-06-13 02:49:03,584] [INFO] Total running time: 0h0m43s