[2023-03-16 06:58:28,751] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:58:28,751] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:58:28,752] [INFO] DQC Reference Directory: /var/lib/cwl/stgce352af7-7e3b-4e0a-9c0a-c6293611468f/dqc_reference
[2023-03-16 06:58:29,820] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:58:29,820] [INFO] Task started: Prodigal
[2023-03-16 06:58:29,820] [INFO] Running command: cat /var/lib/cwl/stg70f7ae3d-5603-4b86-a687-867e4ad799df/OceanDNA-b36417.fa | prodigal -d OceanDNA-b36417/cds.fna -a OceanDNA-b36417/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:58:52,594] [INFO] Task succeeded: Prodigal
[2023-03-16 06:58:52,594] [INFO] Task started: HMMsearch
[2023-03-16 06:58:52,594] [INFO] Running command: hmmsearch --tblout OceanDNA-b36417/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgce352af7-7e3b-4e0a-9c0a-c6293611468f/dqc_reference/reference_markers.hmm OceanDNA-b36417/protein.faa > /dev/null
[2023-03-16 06:58:52,802] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:58:52,803] [INFO] Found 6/6 markers.
[2023-03-16 06:58:52,824] [INFO] Query marker FASTA was written to OceanDNA-b36417/markers.fasta
[2023-03-16 06:58:52,825] [INFO] Task started: Blastn
[2023-03-16 06:58:52,825] [INFO] Running command: blastn -query OceanDNA-b36417/markers.fasta -db /var/lib/cwl/stgce352af7-7e3b-4e0a-9c0a-c6293611468f/dqc_reference/reference_markers.fasta -out OceanDNA-b36417/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:58:53,658] [INFO] Task succeeded: Blastn
[2023-03-16 06:58:53,659] [INFO] Selected 9 target genomes.
[2023-03-16 06:58:53,659] [INFO] Target genome list was writen to OceanDNA-b36417/target_genomes.txt
[2023-03-16 06:58:53,665] [INFO] Task started: fastANI
[2023-03-16 06:58:53,665] [INFO] Running command: fastANI --query /var/lib/cwl/stg70f7ae3d-5603-4b86-a687-867e4ad799df/OceanDNA-b36417.fa --refList OceanDNA-b36417/target_genomes.txt --output OceanDNA-b36417/fastani_result.tsv --threads 1
[2023-03-16 06:59:02,330] [INFO] Task succeeded: fastANI
[2023-03-16 06:59:02,330] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgce352af7-7e3b-4e0a-9c0a-c6293611468f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:59:02,330] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgce352af7-7e3b-4e0a-9c0a-c6293611468f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:59:02,338] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:59:02,338] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 06:59:02,338] [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 venustensis	strain=ISO4	GCA_015356855.1	172371	172371	type	True	91.9638	981	1187	95	below_threshold
Alcanivorax profundimaris	strain=ST75FaO-1	GCA_015265435.1	2735259	2735259	type	True	84.1187	890	1187	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	83.8184	806	1187	95	below_threshold
Alcanivorax gelatiniphagus	strain=MEBiC 08158	GCA_005938655.1	1194167	1194167	type	True	83.7804	854	1187	95	below_threshold
Alcanivorax mobilis	strain=MT13131	GCA_002864685.1	2019569	2019569	type	True	81.8809	768	1187	95	below_threshold
Alcanivorax balearicus	strain=MACL04	GCA_025532145.1	413232	413232	type	True	80.0782	615	1187	95	below_threshold
Alcanivorax limicola	strain=JB21	GCA_019931215.1	2874102	2874102	type	True	77.8649	271	1187	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	77.247	259	1187	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	77.0221	198	1187	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 06:59:02,338] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36417/tc_result.tsv
[2023-03-16 06:59:02,338] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:59:02,338] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:59:02,338] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgce352af7-7e3b-4e0a-9c0a-c6293611468f/dqc_reference/checkm_data
[2023-03-16 06:59:02,339] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:59:02,357] [INFO] Task started: CheckM
[2023-03-16 06:59:02,357] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36417/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36417/checkm_input OceanDNA-b36417/checkm_result
[2023-03-16 06:59:58,938] [INFO] Task succeeded: CheckM
[2023-03-16 06:59:58,939] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:59:58,941] [INFO] ===== Completeness check finished =====
[2023-03-16 06:59:58,941] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:59:58,942] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36417/markers.fasta)
[2023-03-16 06:59:58,943] [INFO] Task started: Blastn
[2023-03-16 06:59:58,943] [INFO] Running command: blastn -query OceanDNA-b36417/markers.fasta -db /var/lib/cwl/stgce352af7-7e3b-4e0a-9c0a-c6293611468f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36417/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 07:00:00,650] [INFO] Task succeeded: Blastn
[2023-03-16 07:00:00,651] [INFO] Selected 8 target genomes.
[2023-03-16 07:00:00,651] [INFO] Target genome list was writen to OceanDNA-b36417/target_genomes_gtdb.txt
[2023-03-16 07:00:00,681] [INFO] Task started: fastANI
[2023-03-16 07:00:00,681] [INFO] Running command: fastANI --query /var/lib/cwl/stg70f7ae3d-5603-4b86-a687-867e4ad799df/OceanDNA-b36417.fa --refList OceanDNA-b36417/target_genomes_gtdb.txt --output OceanDNA-b36417/fastani_result_gtdb.tsv --threads 1
[2023-03-16 07:00:08,632] [INFO] Task succeeded: fastANI
[2023-03-16 07:00:08,638] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 07:00:08,638] [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_002389055.1	s__Alcanivorax sp002389055	92.2486	878	1187	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	96.98	96.27	0.78	0.74	3	-
GCF_015356855.1	s__Alcanivorax venustensis	91.9638	981	1187	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	91.2828	940	1187	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	96.99	96.99	0.93	0.93	2	-
GCF_015265435.1	s__Alcanivorax profundimaris	84.1131	891	1187	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.49	97.23	0.85	0.77	11	-
GCF_005938655.1	s__Alcanivorax gelatiniphagus	83.7837	854	1187	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.53	98.53	0.93	0.93	3	-
GCF_016906305.1	s__Alcanivorax marinus_B	83.7181	857	1187	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016785095.1	s__Alcanivorax marinus_A	82.8413	824	1187	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402545.1	s__Saccharospirillum sp018402545	78.1079	58	1187	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Natronospirillaceae;g__Saccharospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 07:00:08,638] [INFO] GTDB search result was written to OceanDNA-b36417/result_gtdb.tsv
[2023-03-16 07:00:08,638] [INFO] ===== GTDB Search completed =====
[2023-03-16 07:00:08,639] [INFO] DFAST_QC result json was written to OceanDNA-b36417/dqc_result.json
[2023-03-16 07:00:08,640] [INFO] DFAST_QC completed!
[2023-03-16 07:00:08,640] [INFO] Total running time: 0h1m40s