[2023-03-18 05:35:37,309] [INFO] DFAST_QC pipeline started.
[2023-03-18 05:35:37,312] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 05:35:37,312] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0d4807b-df94-45b8-bc8b-75be77a83ef9/dqc_reference
[2023-03-18 05:35:38,963] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 05:35:38,963] [INFO] Task started: Prodigal
[2023-03-18 05:35:38,963] [INFO] Running command: cat /var/lib/cwl/stg3afaaf02-0600-4609-9c00-0c9f4634e1fe/OceanDNA-b20909.fa | prodigal -d OceanDNA-b20909/cds.fna -a OceanDNA-b20909/protein.faa -g 11 -q > /dev/null
[2023-03-18 05:36:10,408] [INFO] Task succeeded: Prodigal
[2023-03-18 05:36:10,408] [INFO] Task started: HMMsearch
[2023-03-18 05:36:10,408] [INFO] Running command: hmmsearch --tblout OceanDNA-b20909/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0d4807b-df94-45b8-bc8b-75be77a83ef9/dqc_reference/reference_markers.hmm OceanDNA-b20909/protein.faa > /dev/null
[2023-03-18 05:36:10,691] [INFO] Task succeeded: HMMsearch
[2023-03-18 05:36:10,692] [INFO] Found 6/6 markers.
[2023-03-18 05:36:10,740] [INFO] Query marker FASTA was written to OceanDNA-b20909/markers.fasta
[2023-03-18 05:36:10,741] [INFO] Task started: Blastn
[2023-03-18 05:36:10,741] [INFO] Running command: blastn -query OceanDNA-b20909/markers.fasta -db /var/lib/cwl/stgd0d4807b-df94-45b8-bc8b-75be77a83ef9/dqc_reference/reference_markers.fasta -out OceanDNA-b20909/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:36:11,472] [INFO] Task succeeded: Blastn
[2023-03-18 05:36:11,474] [INFO] Selected 22 target genomes.
[2023-03-18 05:36:11,475] [INFO] Target genome list was writen to OceanDNA-b20909/target_genomes.txt
[2023-03-18 05:36:11,488] [INFO] Task started: fastANI
[2023-03-18 05:36:11,489] [INFO] Running command: fastANI --query /var/lib/cwl/stg3afaaf02-0600-4609-9c00-0c9f4634e1fe/OceanDNA-b20909.fa --refList OceanDNA-b20909/target_genomes.txt --output OceanDNA-b20909/fastani_result.tsv --threads 1
[2023-03-18 05:36:29,693] [INFO] Task succeeded: fastANI
[2023-03-18 05:36:29,693] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0d4807b-df94-45b8-bc8b-75be77a83ef9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 05:36:29,694] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0d4807b-df94-45b8-bc8b-75be77a83ef9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 05:36:29,706] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 05:36:29,706] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 05:36:29,706] [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
Plesiocystis pacifica	strain=SIR-1	GCA_000170895.1	191768	191768	type	True	75.6306	248	1548	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	75.4693	280	1548	95	below_threshold
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	75.4611	283	1548	95	below_threshold
Myxococcus stipitatus	strain=DSM 14675	GCA_000331735.1	83455	83455	neotype	True	74.7927	73	1548	95	below_threshold
Pelomonas puraquae	strain=CCUG 52769	GCA_002205845.1	431059	431059	type	True	74.7847	67	1548	95	below_threshold
Myxococcus fulvus	strain=NBRC 100333	GCA_007991095.1	33	33	type	True	74.7716	88	1548	95	below_threshold
Myxococcus fulvus	strain=DSM 16525	GCA_900111765.1	33	33	type	True	74.7636	90	1548	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	74.7612	60	1548	95	below_threshold
Luteimonas huabeiensis	strain=HB2	GCA_000559025.1	1244513	1244513	type	True	74.7548	65	1548	95	below_threshold
Lysobacter enzymogenes	strain=ATCC 29487	GCA_900106525.1	69	69	suspected-type	True	74.7277	73	1548	95	below_threshold
Rubrivirga marina	strain=SAORIC-28	GCA_002283365.1	1196024	1196024	type	True	74.7108	92	1548	95	below_threshold
Oharaeibacter diazotrophicus	strain=SM30	GCA_011317485.1	1920512	1920512	type	True	74.7035	70	1548	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	74.6961	90	1548	95	below_threshold
Streptomonospora salina	strain=DSM 44593	GCA_014204715.1	104205	104205	type	True	74.5894	64	1548	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 05:36:29,708] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20909/tc_result.tsv
[2023-03-18 05:36:29,709] [INFO] ===== Taxonomy check completed =====
[2023-03-18 05:36:29,710] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 05:36:29,710] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0d4807b-df94-45b8-bc8b-75be77a83ef9/dqc_reference/checkm_data
[2023-03-18 05:36:29,711] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 05:36:29,724] [INFO] Task started: CheckM
[2023-03-18 05:36:29,724] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20909/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20909/checkm_input OceanDNA-b20909/checkm_result
[2023-03-18 05:37:44,628] [INFO] Task succeeded: CheckM
[2023-03-18 05:37:44,629] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.32%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 05:37:44,714] [INFO] ===== Completeness check finished =====
[2023-03-18 05:37:44,715] [INFO] ===== Start GTDB Search =====
[2023-03-18 05:37:44,715] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20909/markers.fasta)
[2023-03-18 05:37:44,716] [INFO] Task started: Blastn
[2023-03-18 05:37:44,716] [INFO] Running command: blastn -query OceanDNA-b20909/markers.fasta -db /var/lib/cwl/stgd0d4807b-df94-45b8-bc8b-75be77a83ef9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20909/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 05:37:46,078] [INFO] Task succeeded: Blastn
[2023-03-18 05:37:46,080] [INFO] Selected 13 target genomes.
[2023-03-18 05:37:46,080] [INFO] Target genome list was writen to OceanDNA-b20909/target_genomes_gtdb.txt
[2023-03-18 05:37:46,091] [INFO] Task started: fastANI
[2023-03-18 05:37:46,091] [INFO] Running command: fastANI --query /var/lib/cwl/stg3afaaf02-0600-4609-9c00-0c9f4634e1fe/OceanDNA-b20909.fa --refList OceanDNA-b20909/target_genomes_gtdb.txt --output OceanDNA-b20909/fastani_result_gtdb.tsv --threads 1
[2023-03-18 05:38:01,973] [INFO] Task succeeded: fastANI
[2023-03-18 05:38:01,980] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 05:38:01,981] [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_016709225.1	s__Ga0077550 sp016709225	76.303	329	1548	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Ga0077550	95.0	99.66	99.17	0.98	0.94	4	-
GCA_001464385.1	s__Ga0077550 sp001464385	76.1321	354	1548	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Ga0077550	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013812955.1	s__Nannocystis sp013812955	75.7913	159	1548	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000170895.1	s__Plesiocystis pacifica	75.6401	246	1548	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Plesiocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003696955.1	s__J032 sp003696955	75.584	87	1548	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__J032	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002994615.1	s__Enhygromyxa salina_A	75.5238	204	1548	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Enhygromyxa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002994635.1	s__Enhygromyxa salina_B	75.4854	197	1548	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Enhygromyxa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002343915.1	s__Nannocystis exedens	75.4706	280	1548	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	99.98	99.98	1.00	1.00	2	-
GCA_016793465.1	s__Nannocystis sp016793465	75.4565	239	1548	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712315.1	s__JADJRG01 sp016712315	75.3885	153	1548	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__JADJRG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019237945.1	s__JABFXX01 sp019237945	74.7912	131	1548	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__JABFXX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794545.1	s__JABFXX01 sp016794545	74.7711	128	1548	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__JABFXX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 05:38:01,982] [INFO] GTDB search result was written to OceanDNA-b20909/result_gtdb.tsv
[2023-03-18 05:38:01,983] [INFO] ===== GTDB Search completed =====
[2023-03-18 05:38:01,986] [INFO] DFAST_QC result json was written to OceanDNA-b20909/dqc_result.json
[2023-03-18 05:38:01,986] [INFO] DFAST_QC completed!
[2023-03-18 05:38:01,986] [INFO] Total running time: 0h2m25s