[2023-03-15 11:22:20,467] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:22:20,468] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:22:20,468] [INFO] DQC Reference Directory: /var/lib/cwl/stgb373b8ab-53dd-4dce-b6d1-062852a4b74b/dqc_reference
[2023-03-15 11:22:21,949] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:22:21,950] [INFO] Task started: Prodigal
[2023-03-15 11:22:21,950] [INFO] Running command: cat /var/lib/cwl/stga9716b58-75c1-4b97-82d1-9adcabc86547/OceanDNA-b20913.fa | prodigal -d OceanDNA-b20913/cds.fna -a OceanDNA-b20913/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:22:53,741] [INFO] Task succeeded: Prodigal
[2023-03-15 11:22:53,741] [INFO] Task started: HMMsearch
[2023-03-15 11:22:53,741] [INFO] Running command: hmmsearch --tblout OceanDNA-b20913/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb373b8ab-53dd-4dce-b6d1-062852a4b74b/dqc_reference/reference_markers.hmm OceanDNA-b20913/protein.faa > /dev/null
[2023-03-15 11:22:54,055] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:22:54,055] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga9716b58-75c1-4b97-82d1-9adcabc86547/OceanDNA-b20913.fa]
[2023-03-15 11:22:54,106] [INFO] Query marker FASTA was written to OceanDNA-b20913/markers.fasta
[2023-03-15 11:22:54,107] [INFO] Task started: Blastn
[2023-03-15 11:22:54,108] [INFO] Running command: blastn -query OceanDNA-b20913/markers.fasta -db /var/lib/cwl/stgb373b8ab-53dd-4dce-b6d1-062852a4b74b/dqc_reference/reference_markers.fasta -out OceanDNA-b20913/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:22:54,805] [INFO] Task succeeded: Blastn
[2023-03-15 11:22:54,806] [INFO] Selected 28 target genomes.
[2023-03-15 11:22:54,807] [INFO] Target genome list was writen to OceanDNA-b20913/target_genomes.txt
[2023-03-15 11:22:54,825] [INFO] Task started: fastANI
[2023-03-15 11:22:54,825] [INFO] Running command: fastANI --query /var/lib/cwl/stga9716b58-75c1-4b97-82d1-9adcabc86547/OceanDNA-b20913.fa --refList OceanDNA-b20913/target_genomes.txt --output OceanDNA-b20913/fastani_result.tsv --threads 1
[2023-03-15 11:23:21,468] [INFO] Task succeeded: fastANI
[2023-03-15 11:23:21,469] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb373b8ab-53dd-4dce-b6d1-062852a4b74b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:23:21,469] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb373b8ab-53dd-4dce-b6d1-062852a4b74b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:23:21,484] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:23:21,484] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:23:21,484] [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
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	76.8022	698	1647	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	76.7979	710	1647	95	below_threshold
Plesiocystis pacifica	strain=SIR-1	GCA_000170895.1	191768	191768	type	True	76.3567	557	1647	95	below_threshold
Vulgatibacter incomptus	strain=DSM 27710	GCA_001263175.1	1391653	1391653	type	True	75.1822	116	1647	95	below_threshold
Sulfurifustis variabilis	strain=skN76	GCA_002355415.1	1675686	1675686	type	True	75.0061	98	1647	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000420125.1	316997	316997	type	True	74.9388	168	1647	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	74.9348	163	1647	95	below_threshold
Pyxidicoccus trucidator	strain=CA060A	GCA_010894435.1	2709662	2709662	type	True	74.9338	180	1647	95	below_threshold
Polyangium aurulentum	strain=SDU3-1	GCA_005144635.2	2567896	2567896	type	True	74.9336	355	1647	95	below_threshold
Labilithrix luteola	strain=DSM 27648	GCA_001263205.1	1391654	1391654	type	True	74.8721	207	1647	95	below_threshold
Pyxidicoccus caerfyrddinensis	strain=CA032A	GCA_010894405.1	2709663	2709663	type	True	74.8684	208	1647	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	74.8529	175	1647	95	below_threshold
Vulcaniibacterium tengchongense	strain=YIM 77520	GCA_008033455.1	1273429	1273429	type	True	74.8491	168	1647	95	below_threshold
Streptomyces roseicoloratus	strain=TRM44457	GCA_004117935.1	2508722	2508722	type	True	74.8465	190	1647	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	74.7965	267	1647	95	below_threshold
Protaetiibacter larvae	strain=KACC 19322	GCA_008365275.1	2592654	2592654	type	True	74.7805	95	1647	95	below_threshold
Luteibacter yeojuensis	strain=DSM 17673	GCA_011742875.1	345309	345309	type	True	74.7526	70	1647	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	74.7493	154	1647	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	74.7384	149	1647	95	below_threshold
Pleomorphomonas carboxyditropha	strain=SVCO-16	GCA_002770725.1	2023338	2023338	type	True	74.7271	130	1647	95	below_threshold
Aeromicrobium phragmitis	strain=9W16Y-2	GCA_003674095.1	2478914	2478914	type	True	74.7248	78	1647	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	74.7084	126	1647	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	74.6914	149	1647	95	below_threshold
Metallibacterium scheffleri	strain=DKE6	GCA_002077135.1	993689	993689	type	True	74.6838	58	1647	95	below_threshold
Metallibacterium scheffleri	strain=DSM 24874	GCA_004798955.1	993689	993689	type	True	74.6826	56	1647	95	below_threshold
Streptomyces lunaelactis	strain=MM109	GCA_003054555.1	1535768	1535768	type	True	74.67	143	1647	95	below_threshold
Rhodanobacter thiooxydans	strain=LCS2	GCA_000264375.1	416169	416169	type	True	74.6137	61	1647	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:23:21,484] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20913/tc_result.tsv
[2023-03-15 11:23:21,484] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:23:21,484] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:23:21,484] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb373b8ab-53dd-4dce-b6d1-062852a4b74b/dqc_reference/checkm_data
[2023-03-15 11:23:21,485] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:23:21,615] [INFO] Task started: CheckM
[2023-03-15 11:23:21,615] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20913/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20913/checkm_input OceanDNA-b20913/checkm_result
[2023-03-15 11:24:37,456] [INFO] Task succeeded: CheckM
[2023-03-15 11:24:37,457] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 4.92%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:24:37,461] [INFO] ===== Completeness check finished =====
[2023-03-15 11:24:37,461] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:24:37,461] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20913/markers.fasta)
[2023-03-15 11:24:37,461] [INFO] Task started: Blastn
[2023-03-15 11:24:37,461] [INFO] Running command: blastn -query OceanDNA-b20913/markers.fasta -db /var/lib/cwl/stgb373b8ab-53dd-4dce-b6d1-062852a4b74b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20913/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:24:38,625] [INFO] Task succeeded: Blastn
[2023-03-15 11:24:38,625] [INFO] Selected 18 target genomes.
[2023-03-15 11:24:38,626] [INFO] Target genome list was writen to OceanDNA-b20913/target_genomes_gtdb.txt
[2023-03-15 11:24:38,644] [INFO] Task started: fastANI
[2023-03-15 11:24:38,645] [INFO] Running command: fastANI --query /var/lib/cwl/stga9716b58-75c1-4b97-82d1-9adcabc86547/OceanDNA-b20913.fa --refList OceanDNA-b20913/target_genomes_gtdb.txt --output OceanDNA-b20913/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:25:02,756] [INFO] Task succeeded: fastANI
[2023-03-15 11:25:02,766] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:25:02,766] [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_013812955.1	s__Nannocystis sp013812955	77.2151	462	1647	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793465.1	s__Nannocystis sp016793465	76.8822	691	1647	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714285.1	s__Nannocystis sp016714285	76.8661	573	1647	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	99.25	99.25	0.96	0.96	2	-
GCF_002343915.1	s__Nannocystis exedens	76.788	703	1647	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002994615.1	s__Enhygromyxa salina_A	76.3855	542	1647	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Enhygromyxa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712315.1	s__JADJRG01 sp016712315	76.3575	468	1647	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__JADJRG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000170895.1	s__Plesiocystis pacifica	76.3352	558	1647	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Plesiocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002994635.1	s__Enhygromyxa salina_B	76.0928	485	1647	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Enhygromyxa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737335.2	s__Enhygromyxa salina_C	75.9741	441	1647	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Enhygromyxa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709225.1	s__Ga0077550 sp016709225	75.9467	533	1647	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	75.8301	560	1647	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Ga0077550	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001263175.1	s__Vulgatibacter incomptus	75.1838	116	1647	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Vulgatibacteraceae;g__Vulgatibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016717005.1	s__UBA2376 sp016717005	75.1473	490	1647	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422205.1	s__Desulfohalovibrio sp000422205	74.8093	75	1647	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfohalovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003139415.1	s__Palsa-1150 sp003139415	74.7775	139	1647	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Palsa-1150	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003153495.1	s__Palsa-1150 sp003153495	74.7202	152	1647	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Palsa-1150	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:25:02,766] [INFO] GTDB search result was written to OceanDNA-b20913/result_gtdb.tsv
[2023-03-15 11:25:02,767] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:25:02,769] [INFO] DFAST_QC result json was written to OceanDNA-b20913/dqc_result.json
[2023-03-15 11:25:02,769] [INFO] DFAST_QC completed!
[2023-03-15 11:25:02,769] [INFO] Total running time: 0h2m42s