[2023-03-14 13:09:10,215] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:09:10,215] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:09:10,215] [INFO] DQC Reference Directory: /var/lib/cwl/stg55c11bc0-ff10-434f-9bf4-192fbca65b19/dqc_reference
[2023-03-14 13:09:11,398] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:09:11,399] [INFO] Task started: Prodigal
[2023-03-14 13:09:11,399] [INFO] Running command: cat /var/lib/cwl/stg9d30dbe3-b779-4478-a483-87af0846adaa/OceanDNA-b36481.fa | prodigal -d OceanDNA-b36481/cds.fna -a OceanDNA-b36481/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:09:45,525] [INFO] Task succeeded: Prodigal
[2023-03-14 13:09:45,525] [INFO] Task started: HMMsearch
[2023-03-14 13:09:45,525] [INFO] Running command: hmmsearch --tblout OceanDNA-b36481/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg55c11bc0-ff10-434f-9bf4-192fbca65b19/dqc_reference/reference_markers.hmm OceanDNA-b36481/protein.faa > /dev/null
[2023-03-14 13:09:45,909] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:09:45,910] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9d30dbe3-b779-4478-a483-87af0846adaa/OceanDNA-b36481.fa]
[2023-03-14 13:09:45,932] [INFO] Query marker FASTA was written to OceanDNA-b36481/markers.fasta
[2023-03-14 13:09:45,934] [INFO] Task started: Blastn
[2023-03-14 13:09:45,934] [INFO] Running command: blastn -query OceanDNA-b36481/markers.fasta -db /var/lib/cwl/stg55c11bc0-ff10-434f-9bf4-192fbca65b19/dqc_reference/reference_markers.fasta -out OceanDNA-b36481/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:09:46,733] [INFO] Task succeeded: Blastn
[2023-03-14 13:09:46,734] [INFO] Selected 11 target genomes.
[2023-03-14 13:09:46,734] [INFO] Target genome list was writen to OceanDNA-b36481/target_genomes.txt
[2023-03-14 13:09:46,741] [INFO] Task started: fastANI
[2023-03-14 13:09:46,741] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d30dbe3-b779-4478-a483-87af0846adaa/OceanDNA-b36481.fa --refList OceanDNA-b36481/target_genomes.txt --output OceanDNA-b36481/fastani_result.tsv --threads 1
[2023-03-14 13:09:56,407] [INFO] Task succeeded: fastANI
[2023-03-14 13:09:56,407] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg55c11bc0-ff10-434f-9bf4-192fbca65b19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:09:56,407] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg55c11bc0-ff10-434f-9bf4-192fbca65b19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:09:56,415] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2023-03-14 13:09:56,415] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-14 13:09:56,415] [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 gelatiniphagus	strain=MEBiC 08158	GCA_005938655.1	1194167	1194167	type	True	98.6311	1084	1168	95	conclusive
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	90.1655	883	1168	95	below_threshold
Alcanivorax profundimaris	strain=ST75FaO-1	GCA_015265435.1	2735259	2735259	type	True	87.6482	933	1168	95	below_threshold
Alcanivorax venustensis	strain=ISO4	GCA_015356855.1	172371	172371	type	True	84.288	765	1168	95	below_threshold
Alcanivorax mobilis	strain=MT13131	GCA_002864685.1	2019569	2019569	type	True	81.8867	770	1168	95	below_threshold
Alcanivorax balearicus	strain=MACL04	GCA_025532145.1	413232	413232	type	True	80.3837	639	1168	95	below_threshold
Alcanivorax xenomutans	strain=JC109	GCA_900217905.1	1094342	1094342	type	True	80.3218	629	1168	95	below_threshold
Alcanivorax hongdengensis	strain=A-11-3	GCA_000300995.1	519051	519051	type	True	79.9927	508	1168	95	below_threshold
Alcanivorax limicola	strain=JB21	GCA_019931215.1	2874102	2874102	type	True	77.8979	283	1168	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	77.5928	274	1168	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	77.0368	256	1168	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 13:09:56,416] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36481/tc_result.tsv
[2023-03-14 13:09:56,416] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:09:56,416] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:09:56,416] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg55c11bc0-ff10-434f-9bf4-192fbca65b19/dqc_reference/checkm_data
[2023-03-14 13:09:56,417] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:09:56,807] [INFO] Task started: CheckM
[2023-03-14 13:09:56,807] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36481/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36481/checkm_input OceanDNA-b36481/checkm_result
[2023-03-14 13:10:58,072] [INFO] Task succeeded: CheckM
[2023-03-14 13:10:58,072] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 13:10:58,075] [INFO] ===== Completeness check finished =====
[2023-03-14 13:10:58,075] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:10:58,075] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36481/markers.fasta)
[2023-03-14 13:10:58,076] [INFO] Task started: Blastn
[2023-03-14 13:10:58,076] [INFO] Running command: blastn -query OceanDNA-b36481/markers.fasta -db /var/lib/cwl/stg55c11bc0-ff10-434f-9bf4-192fbca65b19/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36481/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:10:59,476] [INFO] Task succeeded: Blastn
[2023-03-14 13:10:59,476] [INFO] Selected 7 target genomes.
[2023-03-14 13:10:59,477] [INFO] Target genome list was writen to OceanDNA-b36481/target_genomes_gtdb.txt
[2023-03-14 13:10:59,484] [INFO] Task started: fastANI
[2023-03-14 13:10:59,484] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d30dbe3-b779-4478-a483-87af0846adaa/OceanDNA-b36481.fa --refList OceanDNA-b36481/target_genomes_gtdb.txt --output OceanDNA-b36481/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:11:06,338] [INFO] Task succeeded: fastANI
[2023-03-14 13:11:06,343] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 13:11:06,344] [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_005938655.1	s__Alcanivorax gelatiniphagus	98.615	1085	1168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.53	98.53	0.93	0.93	3	conclusive
GCF_016906305.1	s__Alcanivorax marinus_B	90.2334	977	1168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015265435.1	s__Alcanivorax profundimaris	87.6343	934	1168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.49	97.23	0.85	0.77	11	-
GCF_016785095.1	s__Alcanivorax marinus_A	86.9271	952	1168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015356855.1	s__Alcanivorax venustensis	84.2753	766	1168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.73	95.38	0.91	0.87	46	-
GCA_017794945.1	s__Alcanivorax sp009711585	84.0	693	1168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	96.99	96.99	0.93	0.93	2	-
GCF_004360225.1	s__Alcanivorax sp004360225	80.2028	623	1168	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	99.14	99.14	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-03-14 13:11:06,344] [INFO] GTDB search result was written to OceanDNA-b36481/result_gtdb.tsv
[2023-03-14 13:11:06,344] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:11:06,345] [INFO] DFAST_QC result json was written to OceanDNA-b36481/dqc_result.json
[2023-03-14 13:11:06,346] [INFO] DFAST_QC completed!
[2023-03-14 13:11:06,346] [INFO] Total running time: 0h1m56s