[2023-03-15 08:59:47,054] [INFO] DFAST_QC pipeline started.
[2023-03-15 08:59:47,054] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 08:59:47,054] [INFO] DQC Reference Directory: /var/lib/cwl/stg173462c3-c77a-48c1-b87a-b4d76bb6ed90/dqc_reference
[2023-03-15 08:59:48,171] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 08:59:48,171] [INFO] Task started: Prodigal
[2023-03-15 08:59:48,171] [INFO] Running command: cat /var/lib/cwl/stg010b8be7-14a0-4641-b46d-018f21df75ff/OceanDNA-b34693.fa | prodigal -d OceanDNA-b34693/cds.fna -a OceanDNA-b34693/protein.faa -g 11 -q > /dev/null
[2023-03-15 09:00:08,597] [INFO] Task succeeded: Prodigal
[2023-03-15 09:00:08,598] [INFO] Task started: HMMsearch
[2023-03-15 09:00:08,598] [INFO] Running command: hmmsearch --tblout OceanDNA-b34693/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg173462c3-c77a-48c1-b87a-b4d76bb6ed90/dqc_reference/reference_markers.hmm OceanDNA-b34693/protein.faa > /dev/null
[2023-03-15 09:00:08,835] [INFO] Task succeeded: HMMsearch
[2023-03-15 09:00:08,836] [INFO] Found 6/6 markers.
[2023-03-15 09:00:08,859] [INFO] Query marker FASTA was written to OceanDNA-b34693/markers.fasta
[2023-03-15 09:00:08,860] [INFO] Task started: Blastn
[2023-03-15 09:00:08,860] [INFO] Running command: blastn -query OceanDNA-b34693/markers.fasta -db /var/lib/cwl/stg173462c3-c77a-48c1-b87a-b4d76bb6ed90/dqc_reference/reference_markers.fasta -out OceanDNA-b34693/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:00:09,522] [INFO] Task succeeded: Blastn
[2023-03-15 09:00:09,523] [INFO] Selected 16 target genomes.
[2023-03-15 09:00:09,523] [INFO] Target genome list was writen to OceanDNA-b34693/target_genomes.txt
[2023-03-15 09:00:09,534] [INFO] Task started: fastANI
[2023-03-15 09:00:09,534] [INFO] Running command: fastANI --query /var/lib/cwl/stg010b8be7-14a0-4641-b46d-018f21df75ff/OceanDNA-b34693.fa --refList OceanDNA-b34693/target_genomes.txt --output OceanDNA-b34693/fastani_result.tsv --threads 1
[2023-03-15 09:00:21,592] [INFO] Task succeeded: fastANI
[2023-03-15 09:00:21,593] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg173462c3-c77a-48c1-b87a-b4d76bb6ed90/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 09:00:21,593] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg173462c3-c77a-48c1-b87a-b4d76bb6ed90/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 09:00:21,600] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 09:00:21,600] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 09:00:21,601] [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
Cognaticolwellia mytili	strain=KCTC 52417	GCA_002104475.1	1888913	1888913	type	True	79.9558	635	1289	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_002104455.1	641665	641665	type	True	79.3599	481	1289	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_900109795.1	641665	641665	type	True	79.3194	479	1289	95	below_threshold
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	78.3292	240	1289	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	78.2562	208	1289	95	below_threshold
Colwellia hornerae	strain=ACAM 607	GCA_007954355.1	89402	89402	type	True	78.2189	320	1289	95	below_threshold
Thalassotalea piscium	strain=DSM 26287	GCA_014207645.1	1230533	1230533	type	True	78.053	227	1289	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	78.0276	215	1289	95	below_threshold
Thalassotalea marina	strain=KCTC 42731	GCA_014656435.1	1673741	1673741	type	True	77.3722	171	1289	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	76.7458	85	1289	95	below_threshold
Shewanella ulleungensis	strain=KCTC 62130	GCA_023283965.1	2282699	2282699	type	True	76.1101	70	1289	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 09:00:21,601] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34693/tc_result.tsv
[2023-03-15 09:00:21,601] [INFO] ===== Taxonomy check completed =====
[2023-03-15 09:00:21,601] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 09:00:21,601] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg173462c3-c77a-48c1-b87a-b4d76bb6ed90/dqc_reference/checkm_data
[2023-03-15 09:00:21,602] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 09:00:21,607] [INFO] Task started: CheckM
[2023-03-15 09:00:21,607] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34693/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34693/checkm_input OceanDNA-b34693/checkm_result
[2023-03-15 09:01:12,928] [INFO] Task succeeded: CheckM
[2023-03-15 09:01:12,928] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 09:01:12,931] [INFO] ===== Completeness check finished =====
[2023-03-15 09:01:12,931] [INFO] ===== Start GTDB Search =====
[2023-03-15 09:01:12,931] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34693/markers.fasta)
[2023-03-15 09:01:12,931] [INFO] Task started: Blastn
[2023-03-15 09:01:12,931] [INFO] Running command: blastn -query OceanDNA-b34693/markers.fasta -db /var/lib/cwl/stg173462c3-c77a-48c1-b87a-b4d76bb6ed90/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34693/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 09:01:13,975] [INFO] Task succeeded: Blastn
[2023-03-15 09:01:13,976] [INFO] Selected 10 target genomes.
[2023-03-15 09:01:13,976] [INFO] Target genome list was writen to OceanDNA-b34693/target_genomes_gtdb.txt
[2023-03-15 09:01:14,012] [INFO] Task started: fastANI
[2023-03-15 09:01:14,012] [INFO] Running command: fastANI --query /var/lib/cwl/stg010b8be7-14a0-4641-b46d-018f21df75ff/OceanDNA-b34693.fa --refList OceanDNA-b34693/target_genomes_gtdb.txt --output OceanDNA-b34693/fastani_result_gtdb.tsv --threads 1
[2023-03-15 09:01:22,948] [INFO] Task succeeded: fastANI
[2023-03-15 09:01:22,954] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 09:01:22,954] [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_002000025.1	s__Cognaticolwellia aestuarii	86.9511	1019	1289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003354085.1	s__Cognaticolwellia sp003354085	83.3607	838	1289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003971255.1	s__Cognaticolwellia sp003971255	82.7816	829	1289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014077505.1	s__Cognaticolwellia sp014077505	81.2505	676	1289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002076895.1	s__Cognaticolwellia beringensis	81.0179	723	1289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003061515.1	s__Cognaticolwellia sp003061515	80.899	646	1289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	98.05	98.05	0.90	0.90	2	-
GCF_002077175.1	s__Cognaticolwellia sp002077175	80.794	709	1289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014077005.1	s__Cognaticolwellia sp014077005	80.7517	667	1289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	98.22	95.22	0.95	0.87	11	-
GCF_014077095.1	s__Cognaticolwellia sp014077095	80.698	645	1289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002104535.1	s__Cognaticolwellia sediminilitoris	80.5992	653	1289	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 09:01:22,954] [INFO] GTDB search result was written to OceanDNA-b34693/result_gtdb.tsv
[2023-03-15 09:01:22,955] [INFO] ===== GTDB Search completed =====
[2023-03-15 09:01:22,956] [INFO] DFAST_QC result json was written to OceanDNA-b34693/dqc_result.json
[2023-03-15 09:01:22,956] [INFO] DFAST_QC completed!
[2023-03-15 09:01:22,956] [INFO] Total running time: 0h1m36s