[2023-03-14 12:25:41,439] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:25:41,439] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:25:41,440] [INFO] DQC Reference Directory: /var/lib/cwl/stg818d9215-5fb8-424c-b0cb-f78068e1bc37/dqc_reference
[2023-03-14 12:25:42,649] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:25:42,650] [INFO] Task started: Prodigal
[2023-03-14 12:25:42,650] [INFO] Running command: cat /var/lib/cwl/stgc68cf64f-597f-4d59-91d1-4d1b8259b5e3/OceanDNA-a4637.fa | prodigal -d OceanDNA-a4637/cds.fna -a OceanDNA-a4637/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:25:49,856] [INFO] Task succeeded: Prodigal
[2023-03-14 12:25:49,857] [INFO] Task started: HMMsearch
[2023-03-14 12:25:49,857] [INFO] Running command: hmmsearch --tblout OceanDNA-a4637/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg818d9215-5fb8-424c-b0cb-f78068e1bc37/dqc_reference/reference_markers.hmm OceanDNA-a4637/protein.faa > /dev/null
[2023-03-14 12:25:50,026] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:25:50,026] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgc68cf64f-597f-4d59-91d1-4d1b8259b5e3/OceanDNA-a4637.fa]
[2023-03-14 12:25:50,039] [INFO] Query marker FASTA was written to OceanDNA-a4637/markers.fasta
[2023-03-14 12:25:50,039] [INFO] Task started: Blastn
[2023-03-14 12:25:50,039] [INFO] Running command: blastn -query OceanDNA-a4637/markers.fasta -db /var/lib/cwl/stg818d9215-5fb8-424c-b0cb-f78068e1bc37/dqc_reference/reference_markers.fasta -out OceanDNA-a4637/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:25:50,518] [INFO] Task succeeded: Blastn
[2023-03-14 12:25:50,518] [INFO] Selected 4 target genomes.
[2023-03-14 12:25:50,519] [INFO] Target genome list was writen to OceanDNA-a4637/target_genomes.txt
[2023-03-14 12:25:50,522] [INFO] Task started: fastANI
[2023-03-14 12:25:50,522] [INFO] Running command: fastANI --query /var/lib/cwl/stgc68cf64f-597f-4d59-91d1-4d1b8259b5e3/OceanDNA-a4637.fa --refList OceanDNA-a4637/target_genomes.txt --output OceanDNA-a4637/fastani_result.tsv --threads 1
[2023-03-14 12:25:52,498] [INFO] Task succeeded: fastANI
[2023-03-14 12:25:52,499] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg818d9215-5fb8-424c-b0cb-f78068e1bc37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:25:52,499] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg818d9215-5fb8-424c-b0cb-f78068e1bc37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:25:52,499] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:25:52,499] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 12:25:52,499] [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
--------------------------------------------------------------------------------
[2023-03-14 12:25:52,499] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4637/tc_result.tsv
[2023-03-14 12:25:52,499] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:25:52,499] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:25:52,500] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg818d9215-5fb8-424c-b0cb-f78068e1bc37/dqc_reference/checkm_data
[2023-03-14 12:25:52,503] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:25:53,222] [INFO] Task started: CheckM
[2023-03-14 12:25:53,222] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4637/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4637/checkm_input OceanDNA-a4637/checkm_result
[2023-03-14 12:26:16,498] [INFO] Task succeeded: CheckM
[2023-03-14 12:26:16,498] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.57%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:26:16,507] [INFO] ===== Completeness check finished =====
[2023-03-14 12:26:16,508] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:26:16,508] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4637/markers.fasta)
[2023-03-14 12:26:16,509] [INFO] Task started: Blastn
[2023-03-14 12:26:16,509] [INFO] Running command: blastn -query OceanDNA-a4637/markers.fasta -db /var/lib/cwl/stg818d9215-5fb8-424c-b0cb-f78068e1bc37/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4637/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:26:16,954] [INFO] Task succeeded: Blastn
[2023-03-14 12:26:16,955] [INFO] Selected 5 target genomes.
[2023-03-14 12:26:16,955] [INFO] Target genome list was writen to OceanDNA-a4637/target_genomes_gtdb.txt
[2023-03-14 12:26:16,961] [INFO] Task started: fastANI
[2023-03-14 12:26:16,961] [INFO] Running command: fastANI --query /var/lib/cwl/stgc68cf64f-597f-4d59-91d1-4d1b8259b5e3/OceanDNA-a4637.fa --refList OceanDNA-a4637/target_genomes_gtdb.txt --output OceanDNA-a4637/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:26:18,286] [INFO] Task succeeded: fastANI
[2023-03-14 12:26:18,289] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 12:26:18,289] [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_002504435.1	s__MGIIb-O5 sp002504435	99.8363	356	390	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	99.62	99.62	0.76	0.76	2	conclusive
GCA_002498925.1	s__MGIIb-O5 sp002498925	80.9705	267	390	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	99.31	97.86	0.85	0.82	9	-
GCA_002718995.2	s__MGIIb-O5 sp002718995	80.7943	292	390	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	99.42	98.33	0.97	0.95	5	-
GCA_002497985.1	s__MGIIb-O5 sp002497985	79.809	165	390	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	95.38	95.38	0.60	0.60	2	-
--------------------------------------------------------------------------------
[2023-03-14 12:26:18,290] [INFO] GTDB search result was written to OceanDNA-a4637/result_gtdb.tsv
[2023-03-14 12:26:18,290] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:26:18,290] [INFO] DFAST_QC result json was written to OceanDNA-a4637/dqc_result.json
[2023-03-14 12:26:18,290] [INFO] DFAST_QC completed!
[2023-03-14 12:26:18,290] [INFO] Total running time: 0h0m37s