[2023-03-18 21:08:06,176] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:08:06,176] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:08:06,176] [INFO] DQC Reference Directory: /var/lib/cwl/stgc711966c-7617-422d-b264-91481299970d/dqc_reference
[2023-03-18 21:08:07,253] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:08:07,254] [INFO] Task started: Prodigal
[2023-03-18 21:08:07,254] [INFO] Running command: cat /var/lib/cwl/stg1b66f7b1-e574-4ccd-a490-49e5e66c8704/OceanDNA-a2961.fa | prodigal -d OceanDNA-a2961/cds.fna -a OceanDNA-a2961/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:08:15,668] [INFO] Task succeeded: Prodigal
[2023-03-18 21:08:15,668] [INFO] Task started: HMMsearch
[2023-03-18 21:08:15,668] [INFO] Running command: hmmsearch --tblout OceanDNA-a2961/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc711966c-7617-422d-b264-91481299970d/dqc_reference/reference_markers.hmm OceanDNA-a2961/protein.faa > /dev/null
[2023-03-18 21:08:15,824] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:08:15,824] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg1b66f7b1-e574-4ccd-a490-49e5e66c8704/OceanDNA-a2961.fa]
[2023-03-18 21:08:15,835] [INFO] Query marker FASTA was written to OceanDNA-a2961/markers.fasta
[2023-03-18 21:08:15,835] [INFO] Task started: Blastn
[2023-03-18 21:08:15,835] [INFO] Running command: blastn -query OceanDNA-a2961/markers.fasta -db /var/lib/cwl/stgc711966c-7617-422d-b264-91481299970d/dqc_reference/reference_markers.fasta -out OceanDNA-a2961/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:08:16,259] [INFO] Task succeeded: Blastn
[2023-03-18 21:08:16,259] [INFO] Selected 2 target genomes.
[2023-03-18 21:08:16,260] [INFO] Target genome list was writen to OceanDNA-a2961/target_genomes.txt
[2023-03-18 21:08:16,261] [INFO] Task started: fastANI
[2023-03-18 21:08:16,261] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b66f7b1-e574-4ccd-a490-49e5e66c8704/OceanDNA-a2961.fa --refList OceanDNA-a2961/target_genomes.txt --output OceanDNA-a2961/fastani_result.tsv --threads 1
[2023-03-18 21:08:17,725] [INFO] Task succeeded: fastANI
[2023-03-18 21:08:17,725] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc711966c-7617-422d-b264-91481299970d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:08:17,726] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc711966c-7617-422d-b264-91481299970d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:08:17,726] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:08:17,726] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 21:08:17,726] [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
--------------------------------------------------------------------------------
[2023-03-18 21:08:18,254] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2961/tc_result.tsv
[2023-03-18 21:08:18,255] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:08:18,255] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:08:18,255] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc711966c-7617-422d-b264-91481299970d/dqc_reference/checkm_data
[2023-03-18 21:08:18,265] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:08:18,359] [INFO] Task started: CheckM
[2023-03-18 21:08:18,359] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2961/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2961/checkm_input OceanDNA-a2961/checkm_result
[2023-03-18 21:08:44,393] [INFO] Task succeeded: CheckM
[2023-03-18 21:08:44,393] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 53.24%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:08:44,395] [INFO] ===== Completeness check finished =====
[2023-03-18 21:08:44,395] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:08:44,395] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2961/markers.fasta)
[2023-03-18 21:08:44,395] [INFO] Task started: Blastn
[2023-03-18 21:08:44,395] [INFO] Running command: blastn -query OceanDNA-a2961/markers.fasta -db /var/lib/cwl/stgc711966c-7617-422d-b264-91481299970d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2961/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:08:44,838] [INFO] Task succeeded: Blastn
[2023-03-18 21:08:44,838] [INFO] Selected 13 target genomes.
[2023-03-18 21:08:44,838] [INFO] Target genome list was writen to OceanDNA-a2961/target_genomes_gtdb.txt
[2023-03-18 21:08:44,851] [INFO] Task started: fastANI
[2023-03-18 21:08:44,851] [INFO] Running command: fastANI --query /var/lib/cwl/stg1b66f7b1-e574-4ccd-a490-49e5e66c8704/OceanDNA-a2961.fa --refList OceanDNA-a2961/target_genomes_gtdb.txt --output OceanDNA-a2961/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:08:48,659] [INFO] Task succeeded: fastANI
[2023-03-18 21:08:48,666] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 21:08:48,666] [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_002722695.1	s__Poseidonia sp002722695	92.8244	310	382	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	99.22	99.22	0.79	0.79	3	-
GCA_002694525.1	s__Poseidonia sp002694525	81.2767	235	382	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002725275.1	s__Poseidonia sp002725275	79.1359	178	382	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	96.76	96.60	0.76	0.75	3	-
GCA_002497765.1	s__Poseidonia sp002497765	78.7254	196	382	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	99.70	99.65	0.88	0.86	3	-
GCA_002714305.1	s__Poseidonia sp002714305	78.7167	154	382	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	98.69	98.28	0.79	0.76	8	-
GCA_002689105.1	s__Poseidonia sp002689105	77.8745	160	382	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	96.72	96.72	0.80	0.80	2	-
GCA_002502295.1	s__Poseidonia sp002502295	77.7587	151	382	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779705.1	s__Poseidonia sp016779705	77.6924	112	382	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003602475.1	s__Poseidonia sp003602475	77.266	78	382	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	95.17	95.17	0.95	0.95	2	-
GCA_016778305.1	s__Poseidonia sp016778305	76.7901	75	382	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	99.89	99.85	0.97	0.96	5	-
GCA_002494645.1	s__Poseidonia sp002494645	76.6766	83	382	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	99.84	99.84	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-03-18 21:08:48,666] [INFO] GTDB search result was written to OceanDNA-a2961/result_gtdb.tsv
[2023-03-18 21:08:48,666] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:08:48,667] [INFO] DFAST_QC result json was written to OceanDNA-a2961/dqc_result.json
[2023-03-18 21:08:48,667] [INFO] DFAST_QC completed!
[2023-03-18 21:08:48,667] [INFO] Total running time: 0h0m42s