[2023-03-16 14:50:25,386] [INFO] DFAST_QC pipeline started.
[2023-03-16 14:50:25,386] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 14:50:25,386] [INFO] DQC Reference Directory: /var/lib/cwl/stg9fec3cd8-c4c3-4005-b713-49557acca98c/dqc_reference
[2023-03-16 14:50:26,691] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 14:50:26,691] [INFO] Task started: Prodigal
[2023-03-16 14:50:26,691] [INFO] Running command: cat /var/lib/cwl/stg0fdbe7bb-7164-4a97-b4ba-53494e58fdfa/OceanDNA-b4392.fa | prodigal -d OceanDNA-b4392/cds.fna -a OceanDNA-b4392/protein.faa -g 11 -q > /dev/null
[2023-03-16 14:50:34,454] [INFO] Task succeeded: Prodigal
[2023-03-16 14:50:34,454] [INFO] Task started: HMMsearch
[2023-03-16 14:50:34,454] [INFO] Running command: hmmsearch --tblout OceanDNA-b4392/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9fec3cd8-c4c3-4005-b713-49557acca98c/dqc_reference/reference_markers.hmm OceanDNA-b4392/protein.faa > /dev/null
[2023-03-16 14:50:34,607] [INFO] Task succeeded: HMMsearch
[2023-03-16 14:50:34,607] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg0fdbe7bb-7164-4a97-b4ba-53494e58fdfa/OceanDNA-b4392.fa]
[2023-03-16 14:50:34,619] [INFO] Query marker FASTA was written to OceanDNA-b4392/markers.fasta
[2023-03-16 14:50:34,619] [INFO] Task started: Blastn
[2023-03-16 14:50:34,619] [INFO] Running command: blastn -query OceanDNA-b4392/markers.fasta -db /var/lib/cwl/stg9fec3cd8-c4c3-4005-b713-49557acca98c/dqc_reference/reference_markers.fasta -out OceanDNA-b4392/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 14:50:35,112] [INFO] Task succeeded: Blastn
[2023-03-16 14:50:35,113] [INFO] Selected 12 target genomes.
[2023-03-16 14:50:35,113] [INFO] Target genome list was writen to OceanDNA-b4392/target_genomes.txt
[2023-03-16 14:50:35,122] [INFO] Task started: fastANI
[2023-03-16 14:50:35,122] [INFO] Running command: fastANI --query /var/lib/cwl/stg0fdbe7bb-7164-4a97-b4ba-53494e58fdfa/OceanDNA-b4392.fa --refList OceanDNA-b4392/target_genomes.txt --output OceanDNA-b4392/fastani_result.tsv --threads 1
[2023-03-16 14:50:42,185] [INFO] Task succeeded: fastANI
[2023-03-16 14:50:42,185] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9fec3cd8-c4c3-4005-b713-49557acca98c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 14:50:42,185] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9fec3cd8-c4c3-4005-b713-49557acca98c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 14:50:42,186] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 14:50:42,186] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 14:50:42,186] [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
--------------------------------------------------------------------------------
[2023-03-16 14:50:42,186] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4392/tc_result.tsv
[2023-03-16 14:50:42,186] [INFO] ===== Taxonomy check completed =====
[2023-03-16 14:50:42,186] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 14:50:42,186] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9fec3cd8-c4c3-4005-b713-49557acca98c/dqc_reference/checkm_data
[2023-03-16 14:50:42,189] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 14:50:42,192] [INFO] Task started: CheckM
[2023-03-16 14:50:42,192] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4392/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4392/checkm_input OceanDNA-b4392/checkm_result
[2023-03-16 14:51:17,935] [INFO] Task succeeded: CheckM
[2023-03-16 14:51:17,935] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 14:51:17,937] [INFO] ===== Completeness check finished =====
[2023-03-16 14:51:17,938] [INFO] ===== Start GTDB Search =====
[2023-03-16 14:51:17,938] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4392/markers.fasta)
[2023-03-16 14:51:17,938] [INFO] Task started: Blastn
[2023-03-16 14:51:17,938] [INFO] Running command: blastn -query OceanDNA-b4392/markers.fasta -db /var/lib/cwl/stg9fec3cd8-c4c3-4005-b713-49557acca98c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4392/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 14:51:18,816] [INFO] Task succeeded: Blastn
[2023-03-16 14:51:18,817] [INFO] Selected 19 target genomes.
[2023-03-16 14:51:18,817] [INFO] Target genome list was writen to OceanDNA-b4392/target_genomes_gtdb.txt
[2023-03-16 14:51:19,547] [INFO] Task started: fastANI
[2023-03-16 14:51:19,548] [INFO] Running command: fastANI --query /var/lib/cwl/stg0fdbe7bb-7164-4a97-b4ba-53494e58fdfa/OceanDNA-b4392.fa --refList OceanDNA-b4392/target_genomes_gtdb.txt --output OceanDNA-b4392/fastani_result_gtdb.tsv --threads 1
[2023-03-16 14:51:27,741] [INFO] Task succeeded: fastANI
[2023-03-16 14:51:27,745] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 14:51:27,746] [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_002701745.1	s__MED-G16 sp002701745	97.3424	291	417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	96.78	96.78	0.79	0.79	2	conclusive
GCA_902626505.1	s__MED-G16 sp902626505	84.3092	255	417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002697405.1	s__MED-G16 sp002697405	81.6461	226	417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	98.03	98.03	0.62	0.62	2	-
GCA_002696995.1	s__MED-G16 sp002696995	78.9685	165	417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	95.99	95.99	0.74	0.74	2	-
GCA_002457315.1	s__MED-G16 sp002457315	78.4758	186	417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002692105.1	s__MED-G16 sp002692105	77.4415	125	417	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	97.44	97.02	0.77	0.72	3	-
--------------------------------------------------------------------------------
[2023-03-16 14:51:27,746] [INFO] GTDB search result was written to OceanDNA-b4392/result_gtdb.tsv
[2023-03-16 14:51:27,746] [INFO] ===== GTDB Search completed =====
[2023-03-16 14:51:27,746] [INFO] DFAST_QC result json was written to OceanDNA-b4392/dqc_result.json
[2023-03-16 14:51:27,747] [INFO] DFAST_QC completed!
[2023-03-16 14:51:27,747] [INFO] Total running time: 0h1m2s