[2023-03-16 05:09:10,893] [INFO] DFAST_QC pipeline started.
[2023-03-16 05:09:10,894] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 05:09:10,894] [INFO] DQC Reference Directory: /var/lib/cwl/stg27ddf8df-5676-418e-a606-d54f9c141366/dqc_reference
[2023-03-16 05:09:11,995] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 05:09:11,995] [INFO] Task started: Prodigal
[2023-03-16 05:09:11,996] [INFO] Running command: cat /var/lib/cwl/stg43ee72d0-d095-440f-a0b6-8a98ad6c2226/OceanDNA-b36411.fa | prodigal -d OceanDNA-b36411/cds.fna -a OceanDNA-b36411/protein.faa -g 11 -q > /dev/null
[2023-03-16 05:09:27,501] [INFO] Task succeeded: Prodigal
[2023-03-16 05:09:27,501] [INFO] Task started: HMMsearch
[2023-03-16 05:09:27,501] [INFO] Running command: hmmsearch --tblout OceanDNA-b36411/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg27ddf8df-5676-418e-a606-d54f9c141366/dqc_reference/reference_markers.hmm OceanDNA-b36411/protein.faa > /dev/null
[2023-03-16 05:09:27,688] [INFO] Task succeeded: HMMsearch
[2023-03-16 05:09:27,688] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg43ee72d0-d095-440f-a0b6-8a98ad6c2226/OceanDNA-b36411.fa]
[2023-03-16 05:09:27,709] [INFO] Query marker FASTA was written to OceanDNA-b36411/markers.fasta
[2023-03-16 05:09:27,710] [INFO] Task started: Blastn
[2023-03-16 05:09:27,710] [INFO] Running command: blastn -query OceanDNA-b36411/markers.fasta -db /var/lib/cwl/stg27ddf8df-5676-418e-a606-d54f9c141366/dqc_reference/reference_markers.fasta -out OceanDNA-b36411/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:09:28,354] [INFO] Task succeeded: Blastn
[2023-03-16 05:09:28,355] [INFO] Selected 12 target genomes.
[2023-03-16 05:09:28,355] [INFO] Target genome list was writen to OceanDNA-b36411/target_genomes.txt
[2023-03-16 05:09:28,364] [INFO] Task started: fastANI
[2023-03-16 05:09:28,364] [INFO] Running command: fastANI --query /var/lib/cwl/stg43ee72d0-d095-440f-a0b6-8a98ad6c2226/OceanDNA-b36411.fa --refList OceanDNA-b36411/target_genomes.txt --output OceanDNA-b36411/fastani_result.tsv --threads 1
[2023-03-16 05:09:36,685] [INFO] Task succeeded: fastANI
[2023-03-16 05:09:36,685] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg27ddf8df-5676-418e-a606-d54f9c141366/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 05:09:36,686] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg27ddf8df-5676-418e-a606-d54f9c141366/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 05:09:36,693] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 05:09:36,693] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 05:09:36,693] [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
Alcanivorax jadensis	strain=T9	GCA_000756655.1	64988	64988	type	True	92.874	736	787	95	below_threshold
Alcanivorax hongdengensis	strain=A-11-3	GCA_000300995.1	519051	519051	type	True	80.934	506	787	95	below_threshold
Alcanivorax profundi	strain=MTEO17	GCA_003597125.1	2338368	2338368	type	True	79.9202	451	787	95	below_threshold
Alcanivorax nanhaiticus	strain=19-m-6	GCA_000756665.1	1177154	1177154	type	True	79.8107	441	787	95	below_threshold
Alcanivorax sediminis	strain=PA15-N-34	GCA_009601165.1	2663008	2663008	type	True	79.6513	465	787	95	below_threshold
Alcanivorax borkumensis	strain=SK2	GCA_000009365.1	59754	59754	type	True	79.0933	353	787	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	79.0344	299	787	95	below_threshold
Alcanivorax profundimaris	strain=ST75FaO-1	GCA_015265435.1	2735259	2735259	type	True	78.9937	334	787	95	below_threshold
Alcanivorax balearicus	strain=MACL04	GCA_025532145.1	413232	413232	type	True	78.2451	264	787	95	below_threshold
Alcanivorax limicola	strain=JB21	GCA_019931215.1	2874102	2874102	type	True	77.4411	192	787	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	76.4599	69	787	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	76.4284	68	787	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 05:09:36,694] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36411/tc_result.tsv
[2023-03-16 05:09:36,694] [INFO] ===== Taxonomy check completed =====
[2023-03-16 05:09:36,694] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 05:09:36,694] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg27ddf8df-5676-418e-a606-d54f9c141366/dqc_reference/checkm_data
[2023-03-16 05:09:36,695] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 05:09:36,700] [INFO] Task started: CheckM
[2023-03-16 05:09:36,700] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36411/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36411/checkm_input OceanDNA-b36411/checkm_result
[2023-03-16 05:10:18,013] [INFO] Task succeeded: CheckM
[2023-03-16 05:10:18,013] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.16%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 05:10:18,016] [INFO] ===== Completeness check finished =====
[2023-03-16 05:10:18,016] [INFO] ===== Start GTDB Search =====
[2023-03-16 05:10:18,017] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36411/markers.fasta)
[2023-03-16 05:10:18,018] [INFO] Task started: Blastn
[2023-03-16 05:10:18,018] [INFO] Running command: blastn -query OceanDNA-b36411/markers.fasta -db /var/lib/cwl/stg27ddf8df-5676-418e-a606-d54f9c141366/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36411/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:10:19,022] [INFO] Task succeeded: Blastn
[2023-03-16 05:10:19,023] [INFO] Selected 9 target genomes.
[2023-03-16 05:10:19,024] [INFO] Target genome list was writen to OceanDNA-b36411/target_genomes_gtdb.txt
[2023-03-16 05:10:19,034] [INFO] Task started: fastANI
[2023-03-16 05:10:19,034] [INFO] Running command: fastANI --query /var/lib/cwl/stg43ee72d0-d095-440f-a0b6-8a98ad6c2226/OceanDNA-b36411.fa --refList OceanDNA-b36411/target_genomes_gtdb.txt --output OceanDNA-b36411/fastani_result_gtdb.tsv --threads 1
[2023-03-16 05:10:25,755] [INFO] Task succeeded: fastANI
[2023-03-16 05:10:25,761] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 05:10:25,761] [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
GCF_000756655.1	s__Alcanivorax jadensis	92.874	736	787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.11	97.73	0.92	0.86	7	-
GCA_014762765.1	s__Alcanivorax sp014762765	89.5233	669	787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003862375.1	s__Alcanivorax jadensis_A	89.0056	711	787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	99.67	99.67	0.92	0.92	2	-
GCF_900107995.1	s__Alcanivorax sp900107995	87.2514	711	787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.42	98.03	0.93	0.89	9	-
GCF_000155615.1	s__Alcanivorax sp000155615	81.5271	558	787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.88	97.69	0.92	0.89	4	-
GCA_002733835.1	s__Alcanivorax sp002733835	81.3259	549	787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000300995.1	s__Alcanivorax hongdengensis	80.934	506	787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009882945.1	s__Alcanivorax sp009882945	80.3843	473	787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017794965.1	s__Alcanivorax sp017794965	80.1264	505	787	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 05:10:25,762] [INFO] GTDB search result was written to OceanDNA-b36411/result_gtdb.tsv
[2023-03-16 05:10:25,762] [INFO] ===== GTDB Search completed =====
[2023-03-16 05:10:25,763] [INFO] DFAST_QC result json was written to OceanDNA-b36411/dqc_result.json
[2023-03-16 05:10:25,763] [INFO] DFAST_QC completed!
[2023-03-16 05:10:25,763] [INFO] Total running time: 0h1m15s