[2023-03-15 11:09:10,797] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:09:10,797] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:09:10,797] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d04fecd-ab52-4836-9d71-241b13dd255d/dqc_reference
[2023-03-15 11:09:12,006] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:09:12,006] [INFO] Task started: Prodigal
[2023-03-15 11:09:12,006] [INFO] Running command: cat /var/lib/cwl/stg5077dd7f-ff19-4d73-9015-f75cc96c047d/OceanDNA-b36408.fa | prodigal -d OceanDNA-b36408/cds.fna -a OceanDNA-b36408/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:09:33,617] [INFO] Task succeeded: Prodigal
[2023-03-15 11:09:33,617] [INFO] Task started: HMMsearch
[2023-03-15 11:09:33,617] [INFO] Running command: hmmsearch --tblout OceanDNA-b36408/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d04fecd-ab52-4836-9d71-241b13dd255d/dqc_reference/reference_markers.hmm OceanDNA-b36408/protein.faa > /dev/null
[2023-03-15 11:09:33,873] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:09:33,874] [INFO] Found 6/6 markers.
[2023-03-15 11:09:33,896] [INFO] Query marker FASTA was written to OceanDNA-b36408/markers.fasta
[2023-03-15 11:09:33,897] [INFO] Task started: Blastn
[2023-03-15 11:09:33,897] [INFO] Running command: blastn -query OceanDNA-b36408/markers.fasta -db /var/lib/cwl/stg1d04fecd-ab52-4836-9d71-241b13dd255d/dqc_reference/reference_markers.fasta -out OceanDNA-b36408/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:09:34,725] [INFO] Task succeeded: Blastn
[2023-03-15 11:09:34,726] [INFO] Selected 10 target genomes.
[2023-03-15 11:09:34,726] [INFO] Target genome list was writen to OceanDNA-b36408/target_genomes.txt
[2023-03-15 11:09:34,733] [INFO] Task started: fastANI
[2023-03-15 11:09:34,733] [INFO] Running command: fastANI --query /var/lib/cwl/stg5077dd7f-ff19-4d73-9015-f75cc96c047d/OceanDNA-b36408.fa --refList OceanDNA-b36408/target_genomes.txt --output OceanDNA-b36408/fastani_result.tsv --threads 1
[2023-03-15 11:09:42,472] [INFO] Task succeeded: fastANI
[2023-03-15 11:09:42,473] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d04fecd-ab52-4836-9d71-241b13dd255d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:09:42,473] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d04fecd-ab52-4836-9d71-241b13dd255d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:09:42,480] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:09:42,480] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:09:42,480] [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	87.1219	920	1142	95	below_threshold
Alcanivorax hongdengensis	strain=A-11-3	GCA_000300995.1	519051	519051	type	True	82.0283	678	1142	95	below_threshold
Alcanivorax profundi	strain=MTEO17	GCA_003597125.1	2338368	2338368	type	True	81.2914	631	1142	95	below_threshold
Alcanivorax nanhaiticus	strain=19-m-6	GCA_000756665.1	1177154	1177154	type	True	81.0546	599	1142	95	below_threshold
Alcanivorax sediminis	strain=PA15-N-34	GCA_009601165.1	2663008	2663008	type	True	80.9117	622	1142	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	79.8066	459	1142	95	below_threshold
Alcanivorax balearicus	strain=MACL04	GCA_025532145.1	413232	413232	type	True	79.0805	396	1142	95	below_threshold
Alcanivorax limicola	strain=JB21	GCA_019931215.1	2874102	2874102	type	True	77.7537	256	1142	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_021165935.1	86173	86173	type	True	77.0362	91	1142	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_022554105.1	86173	86173	type	True	76.9723	92	1142	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:09:42,481] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36408/tc_result.tsv
[2023-03-15 11:09:42,481] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:09:42,481] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:09:42,481] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d04fecd-ab52-4836-9d71-241b13dd255d/dqc_reference/checkm_data
[2023-03-15 11:09:42,482] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:09:42,487] [INFO] Task started: CheckM
[2023-03-15 11:09:42,488] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36408/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36408/checkm_input OceanDNA-b36408/checkm_result
[2023-03-15 11:10:36,845] [INFO] Task succeeded: CheckM
[2023-03-15 11:10:36,845] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.89%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:10:36,848] [INFO] ===== Completeness check finished =====
[2023-03-15 11:10:36,848] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:10:36,848] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36408/markers.fasta)
[2023-03-15 11:10:36,849] [INFO] Task started: Blastn
[2023-03-15 11:10:36,849] [INFO] Running command: blastn -query OceanDNA-b36408/markers.fasta -db /var/lib/cwl/stg1d04fecd-ab52-4836-9d71-241b13dd255d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36408/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:10:38,317] [INFO] Task succeeded: Blastn
[2023-03-15 11:10:38,318] [INFO] Selected 9 target genomes.
[2023-03-15 11:10:38,318] [INFO] Target genome list was writen to OceanDNA-b36408/target_genomes_gtdb.txt
[2023-03-15 11:10:38,326] [INFO] Task started: fastANI
[2023-03-15 11:10:38,326] [INFO] Running command: fastANI --query /var/lib/cwl/stg5077dd7f-ff19-4d73-9015-f75cc96c047d/OceanDNA-b36408.fa --refList OceanDNA-b36408/target_genomes_gtdb.txt --output OceanDNA-b36408/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:10:46,275] [INFO] Task succeeded: fastANI
[2023-03-15 11:10:46,281] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:10:46,281] [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_003862375.1	s__Alcanivorax jadensis_A	88.182	891	1142	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	99.67	99.67	0.92	0.92	2	-
GCA_014762765.1	s__Alcanivorax sp014762765	87.257	815	1142	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000756655.1	s__Alcanivorax jadensis	87.1088	922	1142	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.11	97.73	0.92	0.86	7	-
GCF_900107995.1	s__Alcanivorax sp900107995	86.9137	915	1142	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.42	98.03	0.93	0.89	9	-
GCF_000300995.1	s__Alcanivorax hongdengensis	82.0125	680	1142	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	81.5688	688	1142	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	81.442	645	1142	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003597125.1	s__Alcanivorax profundi	81.2876	631	1142	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	99.31	99.31	0.96	0.96	2	-
GCF_000756665.1	s__Alcanivorax nanhaiticus	81.0471	600	1142	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:10:46,281] [INFO] GTDB search result was written to OceanDNA-b36408/result_gtdb.tsv
[2023-03-15 11:10:46,282] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:10:46,283] [INFO] DFAST_QC result json was written to OceanDNA-b36408/dqc_result.json
[2023-03-15 11:10:46,283] [INFO] DFAST_QC completed!
[2023-03-15 11:10:46,283] [INFO] Total running time: 0h1m35s