[2023-06-29 23:37:16,756] [INFO] DFAST_QC pipeline started.
[2023-06-29 23:37:16,758] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 23:37:16,758] [INFO] DQC Reference Directory: /var/lib/cwl/stgd2cc51f5-7f3d-4a70-aa15-a044d66d44ce/dqc_reference
[2023-06-29 23:37:18,015] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 23:37:18,016] [INFO] Task started: Prodigal
[2023-06-29 23:37:18,016] [INFO] Running command: gunzip -c /var/lib/cwl/stg08215fe4-2fc1-4962-9c2e-d40d54a471e5/GCA_903893095.1_freshwater_MAG_---_I1_bin-135_genomic.fna.gz | prodigal -d GCA_903893095.1_freshwater_MAG_---_I1_bin-135_genomic.fna/cds.fna -a GCA_903893095.1_freshwater_MAG_---_I1_bin-135_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 23:37:24,694] [INFO] Task succeeded: Prodigal
[2023-06-29 23:37:24,695] [INFO] Task started: HMMsearch
[2023-06-29 23:37:24,695] [INFO] Running command: hmmsearch --tblout GCA_903893095.1_freshwater_MAG_---_I1_bin-135_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd2cc51f5-7f3d-4a70-aa15-a044d66d44ce/dqc_reference/reference_markers.hmm GCA_903893095.1_freshwater_MAG_---_I1_bin-135_genomic.fna/protein.faa > /dev/null
[2023-06-29 23:37:25,017] [INFO] Task succeeded: HMMsearch
[2023-06-29 23:37:25,019] [INFO] Found 6/6 markers.
[2023-06-29 23:37:25,068] [INFO] Query marker FASTA was written to GCA_903893095.1_freshwater_MAG_---_I1_bin-135_genomic.fna/markers.fasta
[2023-06-29 23:37:25,069] [INFO] Task started: Blastn
[2023-06-29 23:37:25,069] [INFO] Running command: blastn -query GCA_903893095.1_freshwater_MAG_---_I1_bin-135_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2cc51f5-7f3d-4a70-aa15-a044d66d44ce/dqc_reference/reference_markers.fasta -out GCA_903893095.1_freshwater_MAG_---_I1_bin-135_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:37:25,767] [INFO] Task succeeded: Blastn
[2023-06-29 23:37:25,771] [INFO] Selected 29 target genomes.
[2023-06-29 23:37:25,771] [INFO] Target genome list was writen to GCA_903893095.1_freshwater_MAG_---_I1_bin-135_genomic.fna/target_genomes.txt
[2023-06-29 23:37:25,774] [INFO] Task started: fastANI
[2023-06-29 23:37:25,775] [INFO] Running command: fastANI --query /var/lib/cwl/stg08215fe4-2fc1-4962-9c2e-d40d54a471e5/GCA_903893095.1_freshwater_MAG_---_I1_bin-135_genomic.fna.gz --refList GCA_903893095.1_freshwater_MAG_---_I1_bin-135_genomic.fna/target_genomes.txt --output GCA_903893095.1_freshwater_MAG_---_I1_bin-135_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 23:37:43,920] [INFO] Task succeeded: fastANI
[2023-06-29 23:37:43,921] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd2cc51f5-7f3d-4a70-aa15-a044d66d44ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 23:37:43,921] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd2cc51f5-7f3d-4a70-aa15-a044d66d44ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 23:37:43,929] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 23:37:43,929] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 23:37:43,929] [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
Methylovulum miyakonense	strain=HT12	GCA_000384075.1	645578	645578	type	True	77.1925	52	1025	95	below_threshold
Methylobacter marinus	strain=A45	GCA_000383855.1	34058	34058	type	True	77.0672	68	1025	95	below_threshold
Methylobacter tundripaludum	strain=SV96	GCA_000190755.3	173365	173365	type	True	76.9371	105	1025	95	below_threshold
Methylocucumis oryzae	strain=Sn10-6	GCA_000963695.1	1632867	1632867	type	True	76.5579	58	1025	95	below_threshold
Crenothrix polyspora		GCA_900163755.1	360316	360316	reftype	True	76.3948	90	1025	95	below_threshold
Methylovulum psychrotolerans	strain=Sph1	GCA_002923755.1	1704499	1704499	type	True	76.1759	71	1025	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 23:37:43,931] [INFO] DFAST Taxonomy check result was written to GCA_903893095.1_freshwater_MAG_---_I1_bin-135_genomic.fna/tc_result.tsv
[2023-06-29 23:37:43,932] [INFO] ===== Taxonomy check completed =====
[2023-06-29 23:37:43,932] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 23:37:43,933] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd2cc51f5-7f3d-4a70-aa15-a044d66d44ce/dqc_reference/checkm_data
[2023-06-29 23:37:43,934] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 23:37:43,976] [INFO] Task started: CheckM
[2023-06-29 23:37:43,976] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903893095.1_freshwater_MAG_---_I1_bin-135_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903893095.1_freshwater_MAG_---_I1_bin-135_genomic.fna/checkm_input GCA_903893095.1_freshwater_MAG_---_I1_bin-135_genomic.fna/checkm_result
[2023-06-29 23:38:11,223] [INFO] Task succeeded: CheckM
[2023-06-29 23:38:11,224] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 23:38:11,247] [INFO] ===== Completeness check finished =====
[2023-06-29 23:38:11,247] [INFO] ===== Start GTDB Search =====
[2023-06-29 23:38:11,248] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903893095.1_freshwater_MAG_---_I1_bin-135_genomic.fna/markers.fasta)
[2023-06-29 23:38:11,248] [INFO] Task started: Blastn
[2023-06-29 23:38:11,248] [INFO] Running command: blastn -query GCA_903893095.1_freshwater_MAG_---_I1_bin-135_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2cc51f5-7f3d-4a70-aa15-a044d66d44ce/dqc_reference/reference_markers_gtdb.fasta -out GCA_903893095.1_freshwater_MAG_---_I1_bin-135_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 23:38:12,254] [INFO] Task succeeded: Blastn
[2023-06-29 23:38:12,258] [INFO] Selected 11 target genomes.
[2023-06-29 23:38:12,258] [INFO] Target genome list was writen to GCA_903893095.1_freshwater_MAG_---_I1_bin-135_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 23:38:12,261] [INFO] Task started: fastANI
[2023-06-29 23:38:12,261] [INFO] Running command: fastANI --query /var/lib/cwl/stg08215fe4-2fc1-4962-9c2e-d40d54a471e5/GCA_903893095.1_freshwater_MAG_---_I1_bin-135_genomic.fna.gz --refList GCA_903893095.1_freshwater_MAG_---_I1_bin-135_genomic.fna/target_genomes_gtdb.txt --output GCA_903893095.1_freshwater_MAG_---_I1_bin-135_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 23:38:19,911] [INFO] Task succeeded: fastANI
[2023-06-29 23:38:19,932] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 23:38:19,933] [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_003584865.1	s__KS41 sp003584865	96.8574	583	1025	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.03	97.03	0.84	0.75	9	conclusive
GCA_903839855.1	s__KS41 sp903839855	91.8212	738	1025	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.93	99.90	0.95	0.94	3	-
GCA_903859415.1	s__KS41 sp903859415	87.2535	676	1025	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.28	98.83	0.89	0.85	3	-
GCA_903866825.1	s__KS41 sp903866825	86.526	671	1025	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.82	99.82	0.85	0.85	2	-
GCA_903863905.1	s__KS41 sp903863905	80.1744	336	1025	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.63	99.29	0.91	0.83	33	-
GCA_903873165.1	s__KS41 sp903873165	79.5324	280	1025	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.76	99.76	0.93	0.93	2	-
GCA_903873045.1	s__KS41 sp903873045	78.5211	220	1025	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903917345.1	s__KS41 sp903917345	78.2582	217	1025	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.26	98.86	0.95	0.89	10	-
GCA_903903365.1	s__KS41 sp903903365	77.9329	221	1025	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903905335.1	s__KS41 sp903905335	77.3241	146	1025	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	98.98	98.89	0.85	0.85	5	-
GCF_000190755.2	s__Methylobacter_A tundripaludum	76.9846	103	1025	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylobacter_A	95.0	95.80	95.64	0.85	0.80	9	-
--------------------------------------------------------------------------------
[2023-06-29 23:38:19,936] [INFO] GTDB search result was written to GCA_903893095.1_freshwater_MAG_---_I1_bin-135_genomic.fna/result_gtdb.tsv
[2023-06-29 23:38:19,936] [INFO] ===== GTDB Search completed =====
[2023-06-29 23:38:19,940] [INFO] DFAST_QC result json was written to GCA_903893095.1_freshwater_MAG_---_I1_bin-135_genomic.fna/dqc_result.json
[2023-06-29 23:38:19,940] [INFO] DFAST_QC completed!
[2023-06-29 23:38:19,940] [INFO] Total running time: 0h1m3s