[2023-06-05 00:01:35,521] [INFO] DFAST_QC pipeline started.
[2023-06-05 00:01:35,524] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 00:01:35,524] [INFO] DQC Reference Directory: /var/lib/cwl/stgd04ac2ae-83e3-490e-a186-63a12abeb1a9/dqc_reference
[2023-06-05 00:01:37,907] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 00:01:37,908] [INFO] Task started: Prodigal
[2023-06-05 00:01:37,908] [INFO] Running command: gunzip -c /var/lib/cwl/stg7472c886-400b-4a68-9d30-4572b586353c/GCA_902522285.1_AG-895-B06_genomic.fna.gz | prodigal -d GCA_902522285.1_AG-895-B06_genomic.fna/cds.fna -a GCA_902522285.1_AG-895-B06_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 00:01:40,859] [INFO] Task succeeded: Prodigal
[2023-06-05 00:01:40,860] [INFO] Task started: HMMsearch
[2023-06-05 00:01:40,860] [INFO] Running command: hmmsearch --tblout GCA_902522285.1_AG-895-B06_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd04ac2ae-83e3-490e-a186-63a12abeb1a9/dqc_reference/reference_markers.hmm GCA_902522285.1_AG-895-B06_genomic.fna/protein.faa > /dev/null
[2023-06-05 00:01:41,090] [INFO] Task succeeded: HMMsearch
[2023-06-05 00:01:41,092] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg7472c886-400b-4a68-9d30-4572b586353c/GCA_902522285.1_AG-895-B06_genomic.fna.gz]
[2023-06-05 00:01:41,116] [INFO] Query marker FASTA was written to GCA_902522285.1_AG-895-B06_genomic.fna/markers.fasta
[2023-06-05 00:01:41,116] [INFO] Task started: Blastn
[2023-06-05 00:01:41,116] [INFO] Running command: blastn -query GCA_902522285.1_AG-895-B06_genomic.fna/markers.fasta -db /var/lib/cwl/stgd04ac2ae-83e3-490e-a186-63a12abeb1a9/dqc_reference/reference_markers.fasta -out GCA_902522285.1_AG-895-B06_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:01:43,377] [INFO] Task succeeded: Blastn
[2023-06-05 00:01:43,382] [INFO] Selected 10 target genomes.
[2023-06-05 00:01:43,382] [INFO] Target genome list was writen to GCA_902522285.1_AG-895-B06_genomic.fna/target_genomes.txt
[2023-06-05 00:01:43,383] [INFO] Task started: fastANI
[2023-06-05 00:01:43,384] [INFO] Running command: fastANI --query /var/lib/cwl/stg7472c886-400b-4a68-9d30-4572b586353c/GCA_902522285.1_AG-895-B06_genomic.fna.gz --refList GCA_902522285.1_AG-895-B06_genomic.fna/target_genomes.txt --output GCA_902522285.1_AG-895-B06_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 00:01:47,032] [INFO] Task succeeded: fastANI
[2023-06-05 00:01:47,032] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd04ac2ae-83e3-490e-a186-63a12abeb1a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 00:01:47,033] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd04ac2ae-83e3-490e-a186-63a12abeb1a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 00:01:47,036] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 00:01:47,036] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 00:01:47,036] [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
Candidatus Pelagibacter ubique	strain=HTCC1062	GCA_000012345.1	198252	198252	suspected-type	True	78.194	150	333	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 00:01:47,039] [INFO] DFAST Taxonomy check result was written to GCA_902522285.1_AG-895-B06_genomic.fna/tc_result.tsv
[2023-06-05 00:01:47,039] [INFO] ===== Taxonomy check completed =====
[2023-06-05 00:01:47,039] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 00:01:47,039] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd04ac2ae-83e3-490e-a186-63a12abeb1a9/dqc_reference/checkm_data
[2023-06-05 00:01:47,040] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 00:01:47,057] [INFO] Task started: CheckM
[2023-06-05 00:01:47,057] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902522285.1_AG-895-B06_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902522285.1_AG-895-B06_genomic.fna/checkm_input GCA_902522285.1_AG-895-B06_genomic.fna/checkm_result
[2023-06-05 00:02:05,519] [INFO] Task succeeded: CheckM
[2023-06-05 00:02:05,521] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 00:02:05,541] [INFO] ===== Completeness check finished =====
[2023-06-05 00:02:05,542] [INFO] ===== Start GTDB Search =====
[2023-06-05 00:02:05,542] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902522285.1_AG-895-B06_genomic.fna/markers.fasta)
[2023-06-05 00:02:05,543] [INFO] Task started: Blastn
[2023-06-05 00:02:05,543] [INFO] Running command: blastn -query GCA_902522285.1_AG-895-B06_genomic.fna/markers.fasta -db /var/lib/cwl/stgd04ac2ae-83e3-490e-a186-63a12abeb1a9/dqc_reference/reference_markers_gtdb.fasta -out GCA_902522285.1_AG-895-B06_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:02:06,062] [INFO] Task succeeded: Blastn
[2023-06-05 00:02:06,066] [INFO] Selected 17 target genomes.
[2023-06-05 00:02:06,067] [INFO] Target genome list was writen to GCA_902522285.1_AG-895-B06_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 00:02:06,072] [INFO] Task started: fastANI
[2023-06-05 00:02:06,072] [INFO] Running command: fastANI --query /var/lib/cwl/stg7472c886-400b-4a68-9d30-4572b586353c/GCA_902522285.1_AG-895-B06_genomic.fna.gz --refList GCA_902522285.1_AG-895-B06_genomic.fna/target_genomes_gtdb.txt --output GCA_902522285.1_AG-895-B06_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 00:02:09,819] [INFO] Task succeeded: fastANI
[2023-06-05 00:02:09,840] [INFO] Found 17 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-05 00:02:09,841] [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_902596515.1	s__Pelagibacter sp902596515	98.7087	292	333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	97.03	95.14	0.85	0.80	9	inconclusive
GCA_902541825.1	s__Pelagibacter sp902541825	95.1304	208	333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	95.36	95.25	0.66	0.63	4	inconclusive
GCA_902571015.1	s__Pelagibacter sp902571015	94.0885	258	333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902539445.1	s__Pelagibacter sp902539445	94.0701	270	333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902600635.1	s__Pelagibacter sp902600635	93.6335	143	333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902576375.1	s__Pelagibacter sp902576375	93.3161	274	333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902596925.1	s__Pelagibacter sp902596925	92.9268	262	333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	96.28	96.07	0.86	0.84	3	-
GCA_902597725.1	s__Pelagibacter sp902597725	92.5098	192	333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902568855.1	s__Pelagibacter sp902568855	92.0977	138	333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902582845.1	s__Pelagibacter sp902582845	91.4421	222	333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902531765.1	s__Pelagibacter sp902531765	91.3194	249	333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902523125.1	s__Pelagibacter sp902523125	90.878	184	333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101315.1	s__Pelagibacter sp002101315	90.7915	290	333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902557235.1	s__Pelagibacter sp902557235	90.5187	210	333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902524545.1	s__Pelagibacter sp902524545	88.5904	247	333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902625035.1	s__Pelagibacter sp902625035	88.4136	233	333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902633585.1	s__Pelagibacter sp902633585	87.8021	173	333	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 00:02:09,843] [INFO] GTDB search result was written to GCA_902522285.1_AG-895-B06_genomic.fna/result_gtdb.tsv
[2023-06-05 00:02:09,843] [INFO] ===== GTDB Search completed =====
[2023-06-05 00:02:09,847] [INFO] DFAST_QC result json was written to GCA_902522285.1_AG-895-B06_genomic.fna/dqc_result.json
[2023-06-05 00:02:09,847] [INFO] DFAST_QC completed!
[2023-06-05 00:02:09,847] [INFO] Total running time: 0h0m34s