[2023-03-16 04:24:46,331] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:24:46,331] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:24:46,332] [INFO] DQC Reference Directory: /var/lib/cwl/stg223df176-392f-4e41-a810-f8ab183ab4e6/dqc_reference
[2023-03-16 04:24:48,114] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:24:48,115] [INFO] Task started: Prodigal
[2023-03-16 04:24:48,115] [INFO] Running command: cat /var/lib/cwl/stg1a200c8f-5580-419b-a70f-1f54d4fd8075/OceanDNA-b20946.fa | prodigal -d OceanDNA-b20946/cds.fna -a OceanDNA-b20946/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:25:08,291] [INFO] Task succeeded: Prodigal
[2023-03-16 04:25:08,291] [INFO] Task started: HMMsearch
[2023-03-16 04:25:08,291] [INFO] Running command: hmmsearch --tblout OceanDNA-b20946/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg223df176-392f-4e41-a810-f8ab183ab4e6/dqc_reference/reference_markers.hmm OceanDNA-b20946/protein.faa > /dev/null
[2023-03-16 04:25:08,597] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:25:08,598] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg1a200c8f-5580-419b-a70f-1f54d4fd8075/OceanDNA-b20946.fa]
[2023-03-16 04:25:08,632] [INFO] Query marker FASTA was written to OceanDNA-b20946/markers.fasta
[2023-03-16 04:25:08,633] [INFO] Task started: Blastn
[2023-03-16 04:25:08,633] [INFO] Running command: blastn -query OceanDNA-b20946/markers.fasta -db /var/lib/cwl/stg223df176-392f-4e41-a810-f8ab183ab4e6/dqc_reference/reference_markers.fasta -out OceanDNA-b20946/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:25:09,174] [INFO] Task succeeded: Blastn
[2023-03-16 04:25:09,175] [INFO] Selected 23 target genomes.
[2023-03-16 04:25:09,175] [INFO] Target genome list was writen to OceanDNA-b20946/target_genomes.txt
[2023-03-16 04:25:09,195] [INFO] Task started: fastANI
[2023-03-16 04:25:09,195] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a200c8f-5580-419b-a70f-1f54d4fd8075/OceanDNA-b20946.fa --refList OceanDNA-b20946/target_genomes.txt --output OceanDNA-b20946/fastani_result.tsv --threads 1
[2023-03-16 04:25:26,867] [INFO] Task succeeded: fastANI
[2023-03-16 04:25:26,867] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg223df176-392f-4e41-a810-f8ab183ab4e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:25:26,867] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg223df176-392f-4e41-a810-f8ab183ab4e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:25:26,872] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:25:26,872] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:25:26,873] [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
Ideonella livida	strain=TBM-1	GCA_010499455.1	2707176	2707176	type	True	75.0392	66	997	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	75.025	81	997	95	below_threshold
Sandaracinus amylolyticus	strain=DSM 53668	GCA_000737325.2	927083	927083	type	True	74.8548	76	997	95	below_threshold
Thermomonospora curvata	strain=DSM 43183	GCA_000024385.1	2020	2020	type	True	74.8546	67	997	95	below_threshold
Thermomonospora echinospora	strain=DSM 43163	GCA_900108175.1	1992	1992	type	True	74.8379	92	997	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:25:26,873] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20946/tc_result.tsv
[2023-03-16 04:25:26,873] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:25:26,873] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:25:26,873] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg223df176-392f-4e41-a810-f8ab183ab4e6/dqc_reference/checkm_data
[2023-03-16 04:25:26,874] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:25:26,880] [INFO] Task started: CheckM
[2023-03-16 04:25:26,881] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20946/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20946/checkm_input OceanDNA-b20946/checkm_result
[2023-03-16 04:26:17,252] [INFO] Task succeeded: CheckM
[2023-03-16 04:26:17,252] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.59%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:26:17,255] [INFO] ===== Completeness check finished =====
[2023-03-16 04:26:17,256] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:26:17,256] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20946/markers.fasta)
[2023-03-16 04:26:17,257] [INFO] Task started: Blastn
[2023-03-16 04:26:17,257] [INFO] Running command: blastn -query OceanDNA-b20946/markers.fasta -db /var/lib/cwl/stg223df176-392f-4e41-a810-f8ab183ab4e6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20946/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:26:18,033] [INFO] Task succeeded: Blastn
[2023-03-16 04:26:18,034] [INFO] Selected 25 target genomes.
[2023-03-16 04:26:18,034] [INFO] Target genome list was writen to OceanDNA-b20946/target_genomes_gtdb.txt
[2023-03-16 04:26:18,112] [INFO] Task started: fastANI
[2023-03-16 04:26:18,112] [INFO] Running command: fastANI --query /var/lib/cwl/stg1a200c8f-5580-419b-a70f-1f54d4fd8075/OceanDNA-b20946.fa --refList OceanDNA-b20946/target_genomes_gtdb.txt --output OceanDNA-b20946/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:26:37,206] [INFO] Task succeeded: fastANI
[2023-03-16 04:26:37,215] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:26:37,215] [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_003694325.1	s__J125 sp003694325	76.3946	120	997	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__J125	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016717595.1	s__JADKFE01 sp016717595	76.2915	175	997	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__CAJQPC01;g__JADKFE01	95.0	98.32	98.16	0.91	0.88	3	-
GCA_018401435.1	s__M30B51 sp018401435	76.2354	159	997	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__M30B51	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845285.1	s__BH17 sp016845285	76.1743	111	997	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__BH17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792625.1	s__JAEUKK01 sp016792625	75.9506	153	997	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__JAEUKK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903959175.1	s__CAJBVW01 sp903959175	75.9409	163	997	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__CAJBVW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006226595.1	s__M1803 sp006226595	75.8933	144	997	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__GCA-2862545;g__M1803	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875315.1	s__SXON01 sp016875315	75.8816	133	997	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__SXON01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903861005.1	s__CAIOSP01 sp903861005	75.5821	87	997	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__GCA-2862545;g__CAIOSP01	95.0	99.96	99.95	0.97	0.97	4	-
GCA_011376105.1	s__DRPG01 sp011376105	75.5784	93	997	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__GCA-2862545;g__DRPG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794525.1	s__UBA2376 sp016794525	75.073	142	997	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862085.1	s__GCA-2862085 sp002862085	75.0389	55	997	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2862085	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016717005.1	s__UBA2376 sp016717005	74.9683	121	997	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737325.1	s__Sandaracinus amylolyticus	74.8018	74	997	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Sandaracinaceae;g__Sandaracinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000442255.1	s__Salipiger mucosus	74.6753	51	997	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:26:37,216] [INFO] GTDB search result was written to OceanDNA-b20946/result_gtdb.tsv
[2023-03-16 04:26:37,216] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:26:37,217] [INFO] DFAST_QC result json was written to OceanDNA-b20946/dqc_result.json
[2023-03-16 04:26:37,217] [INFO] DFAST_QC completed!
[2023-03-16 04:26:37,217] [INFO] Total running time: 0h1m51s