[2023-03-17 10:48:45,669] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:48:45,670] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:48:45,670] [INFO] DQC Reference Directory: /var/lib/cwl/stg8564d6e2-e3c0-43a4-b25e-57e1c720472c/dqc_reference
[2023-03-17 10:48:46,895] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:48:46,895] [INFO] Task started: Prodigal
[2023-03-17 10:48:46,895] [INFO] Running command: cat /var/lib/cwl/stg6564f9ff-37bc-422a-adc0-9b99c109beb0/OceanDNA-b42782.fa | prodigal -d OceanDNA-b42782/cds.fna -a OceanDNA-b42782/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:48:50,208] [INFO] Task succeeded: Prodigal
[2023-03-17 10:48:50,208] [INFO] Task started: HMMsearch
[2023-03-17 10:48:50,208] [INFO] Running command: hmmsearch --tblout OceanDNA-b42782/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8564d6e2-e3c0-43a4-b25e-57e1c720472c/dqc_reference/reference_markers.hmm OceanDNA-b42782/protein.faa > /dev/null
[2023-03-17 10:48:50,388] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:48:50,388] [INFO] Found 6/6 markers.
[2023-03-17 10:48:50,400] [INFO] Query marker FASTA was written to OceanDNA-b42782/markers.fasta
[2023-03-17 10:48:50,402] [INFO] Task started: Blastn
[2023-03-17 10:48:50,402] [INFO] Running command: blastn -query OceanDNA-b42782/markers.fasta -db /var/lib/cwl/stg8564d6e2-e3c0-43a4-b25e-57e1c720472c/dqc_reference/reference_markers.fasta -out OceanDNA-b42782/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:48:51,138] [INFO] Task succeeded: Blastn
[2023-03-17 10:48:51,139] [INFO] Selected 18 target genomes.
[2023-03-17 10:48:51,139] [INFO] Target genome list was writen to OceanDNA-b42782/target_genomes.txt
[2023-03-17 10:48:51,193] [INFO] Task started: fastANI
[2023-03-17 10:48:51,194] [INFO] Running command: fastANI --query /var/lib/cwl/stg6564f9ff-37bc-422a-adc0-9b99c109beb0/OceanDNA-b42782.fa --refList OceanDNA-b42782/target_genomes.txt --output OceanDNA-b42782/fastani_result.tsv --threads 1
[2023-03-17 10:48:58,199] [INFO] Task succeeded: fastANI
[2023-03-17 10:48:58,200] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8564d6e2-e3c0-43a4-b25e-57e1c720472c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:48:58,200] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8564d6e2-e3c0-43a4-b25e-57e1c720472c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:48:58,201] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:48:58,201] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 10:48:58,201] [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
--------------------------------------------------------------------------------
[2023-03-17 10:48:58,201] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42782/tc_result.tsv
[2023-03-17 10:48:58,202] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:48:58,202] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:48:58,202] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8564d6e2-e3c0-43a4-b25e-57e1c720472c/dqc_reference/checkm_data
[2023-03-17 10:48:58,205] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:48:58,208] [INFO] Task started: CheckM
[2023-03-17 10:48:58,208] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42782/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42782/checkm_input OceanDNA-b42782/checkm_result
[2023-03-17 10:49:13,816] [INFO] Task succeeded: CheckM
[2023-03-17 10:49:13,817] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.93%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-17 10:49:13,819] [INFO] ===== Completeness check finished =====
[2023-03-17 10:49:13,819] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:49:13,819] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42782/markers.fasta)
[2023-03-17 10:49:13,819] [INFO] Task started: Blastn
[2023-03-17 10:49:13,819] [INFO] Running command: blastn -query OceanDNA-b42782/markers.fasta -db /var/lib/cwl/stg8564d6e2-e3c0-43a4-b25e-57e1c720472c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42782/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:49:14,564] [INFO] Task succeeded: Blastn
[2023-03-17 10:49:14,565] [INFO] Selected 18 target genomes.
[2023-03-17 10:49:14,565] [INFO] Target genome list was writen to OceanDNA-b42782/target_genomes_gtdb.txt
[2023-03-17 10:49:15,073] [INFO] Task started: fastANI
[2023-03-17 10:49:15,073] [INFO] Running command: fastANI --query /var/lib/cwl/stg6564f9ff-37bc-422a-adc0-9b99c109beb0/OceanDNA-b42782.fa --refList OceanDNA-b42782/target_genomes_gtdb.txt --output OceanDNA-b42782/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:49:18,625] [INFO] Task succeeded: fastANI
[2023-03-17 10:49:18,631] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 10:49:18,631] [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_004321845.1	s__TMED112 sp004321845	98.8948	163	218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003213455.1	s__TMED112 sp003213455	86.7797	134	218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002684055.1	s__TMED112 sp002684055	82.354	123	218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902619265.1	s__TMED112 sp902619265	79.662	126	218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	96.88	96.64	0.91	0.88	6	-
GCA_002170245.2	s__TMED112 sp002170245	79.4112	121	218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902585315.1	s__TMED112 sp902585315	79.2969	104	218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	96.21	96.04	0.78	0.78	6	-
GCA_003278815.1	s__TMED112 sp003278815	79.2932	115	218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002683115.1	s__TMED112 sp002683115	79.075	76	218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902535365.1	s__TMED112 sp902535365	77.4096	66	218	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__TMED112;g__TMED112	95.0	96.49	95.14	0.87	0.82	7	-
--------------------------------------------------------------------------------
[2023-03-17 10:49:18,632] [INFO] GTDB search result was written to OceanDNA-b42782/result_gtdb.tsv
[2023-03-17 10:49:18,632] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:49:18,633] [INFO] DFAST_QC result json was written to OceanDNA-b42782/dqc_result.json
[2023-03-17 10:49:18,633] [INFO] DFAST_QC completed!
[2023-03-17 10:49:18,633] [INFO] Total running time: 0h0m33s