[2024-01-25 18:44:35,550] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:44:35,551] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:44:35,552] [INFO] DQC Reference Directory: /var/lib/cwl/stg9d67c35f-d020-4993-ac04-c4f0357e0954/dqc_reference
[2024-01-25 18:44:36,656] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:44:36,656] [INFO] Task started: Prodigal
[2024-01-25 18:44:36,657] [INFO] Running command: gunzip -c /var/lib/cwl/stg0e7ea87d-8760-4a21-889a-07693684c63f/GCF_000349205.1_MPLversion1_genomic.fna.gz | prodigal -d GCF_000349205.1_MPLversion1_genomic.fna/cds.fna -a GCF_000349205.1_MPLversion1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:44:43,090] [INFO] Task succeeded: Prodigal
[2024-01-25 18:44:43,090] [INFO] Task started: HMMsearch
[2024-01-25 18:44:43,090] [INFO] Running command: hmmsearch --tblout GCF_000349205.1_MPLversion1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9d67c35f-d020-4993-ac04-c4f0357e0954/dqc_reference/reference_markers.hmm GCF_000349205.1_MPLversion1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:44:43,303] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:44:43,304] [INFO] Found 6/6 markers.
[2024-01-25 18:44:43,326] [INFO] Query marker FASTA was written to GCF_000349205.1_MPLversion1_genomic.fna/markers.fasta
[2024-01-25 18:44:43,327] [INFO] Task started: Blastn
[2024-01-25 18:44:43,327] [INFO] Running command: blastn -query GCF_000349205.1_MPLversion1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d67c35f-d020-4993-ac04-c4f0357e0954/dqc_reference/reference_markers.fasta -out GCF_000349205.1_MPLversion1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:44:43,947] [INFO] Task succeeded: Blastn
[2024-01-25 18:44:43,952] [INFO] Selected 23 target genomes.
[2024-01-25 18:44:43,952] [INFO] Target genome list was writen to GCF_000349205.1_MPLversion1_genomic.fna/target_genomes.txt
[2024-01-25 18:44:43,975] [INFO] Task started: fastANI
[2024-01-25 18:44:43,975] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e7ea87d-8760-4a21-889a-07693684c63f/GCF_000349205.1_MPLversion1_genomic.fna.gz --refList GCF_000349205.1_MPLversion1_genomic.fna/target_genomes.txt --output GCF_000349205.1_MPLversion1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:44:56,179] [INFO] Task succeeded: fastANI
[2024-01-25 18:44:56,180] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9d67c35f-d020-4993-ac04-c4f0357e0954/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:44:56,180] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9d67c35f-d020-4993-ac04-c4f0357e0954/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:44:56,186] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:44:56,186] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:44:56,186] [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
Methylophaga lonarensis	strain=MPL	GCA_000349205.1	999151	999151	type	True	100.0	819	823	95	conclusive
Methylophaga thiooxydans	strain=DMS010	GCA_000156355.1	392484	392484	type	True	77.3923	104	823	95	below_threshold
Methylophaga frappieri	strain=JAM7	GCA_000260965.1	754477	754477	type	True	77.3556	102	823	95	below_threshold
Methylophaga nitratireducenticrescens	strain=JAM1	GCA_000260985.3	754476	754476	type	True	77.2439	150	823	95	below_threshold
Methylophaga aminisulfidivorans	strain=MP	GCA_000214595.2	230105	230105	type	True	77.1419	103	823	95	below_threshold
Methylophaga pinxianii	strain=TMB456	GCA_020447225.1	2881052	2881052	type	True	77.0974	144	823	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:44:56,187] [INFO] DFAST Taxonomy check result was written to GCF_000349205.1_MPLversion1_genomic.fna/tc_result.tsv
[2024-01-25 18:44:56,187] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:44:56,187] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:44:56,188] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9d67c35f-d020-4993-ac04-c4f0357e0954/dqc_reference/checkm_data
[2024-01-25 18:44:56,188] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:44:56,218] [INFO] Task started: CheckM
[2024-01-25 18:44:56,218] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000349205.1_MPLversion1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000349205.1_MPLversion1_genomic.fna/checkm_input GCF_000349205.1_MPLversion1_genomic.fna/checkm_result
[2024-01-25 18:45:21,259] [INFO] Task succeeded: CheckM
[2024-01-25 18:45:21,260] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:45:21,281] [INFO] ===== Completeness check finished =====
[2024-01-25 18:45:21,281] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:45:21,282] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000349205.1_MPLversion1_genomic.fna/markers.fasta)
[2024-01-25 18:45:21,282] [INFO] Task started: Blastn
[2024-01-25 18:45:21,282] [INFO] Running command: blastn -query GCF_000349205.1_MPLversion1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d67c35f-d020-4993-ac04-c4f0357e0954/dqc_reference/reference_markers_gtdb.fasta -out GCF_000349205.1_MPLversion1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:45:22,350] [INFO] Task succeeded: Blastn
[2024-01-25 18:45:22,353] [INFO] Selected 21 target genomes.
[2024-01-25 18:45:22,353] [INFO] Target genome list was writen to GCF_000349205.1_MPLversion1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:45:22,389] [INFO] Task started: fastANI
[2024-01-25 18:45:22,390] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e7ea87d-8760-4a21-889a-07693684c63f/GCF_000349205.1_MPLversion1_genomic.fna.gz --refList GCF_000349205.1_MPLversion1_genomic.fna/target_genomes_gtdb.txt --output GCF_000349205.1_MPLversion1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:45:33,103] [INFO] Task succeeded: fastANI
[2024-01-25 18:45:33,110] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:45:33,111] [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_000349205.1	s__Methylophaga lonarensis	100.0	819	823	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_007117275.1	s__Methylophaga sp007117275	84.1364	254	823	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002696735.1	s__Methylophaga sp002696735	77.4577	161	823	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	98.51	97.89	0.93	0.90	20	-
GCF_000260965.1	s__Methylophaga frappieri	77.3556	102	823	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009711715.1	s__Methylophaga sp009711715	77.3533	137	823	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002363955.1	s__Methylophaga sp002363955	77.2926	159	823	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	98.95	98.64	0.94	0.91	14	-
GCF_000260985.4	s__Methylophaga nitratireducenticrescens	77.2439	150	823	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	99.21	99.21	0.92	0.92	2	-
GCA_002354555.1	s__Methylophaga sp002354555	76.9449	136	823	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	98.87	98.17	0.91	0.88	3	-
GCA_014762585.1	s__Methylophaga sp014762585	76.8883	122	823	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706095.1	s__Methylophaga sp002706095	76.868	110	823	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrosococcales;f__Methylophagaceae;g__Methylophaga	95.0	98.12	97.28	0.92	0.89	8	-
--------------------------------------------------------------------------------
[2024-01-25 18:45:33,113] [INFO] GTDB search result was written to GCF_000349205.1_MPLversion1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:45:33,114] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:45:33,116] [INFO] DFAST_QC result json was written to GCF_000349205.1_MPLversion1_genomic.fna/dqc_result.json
[2024-01-25 18:45:33,116] [INFO] DFAST_QC completed!
[2024-01-25 18:45:33,116] [INFO] Total running time: 0h0m58s