[2023-03-18 08:31:56,307] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:31:56,307] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:31:56,307] [INFO] DQC Reference Directory: /var/lib/cwl/stg2856fde7-2c38-4c66-bb29-dc852d325d65/dqc_reference
[2023-03-18 08:31:57,415] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:31:57,416] [INFO] Task started: Prodigal
[2023-03-18 08:31:57,416] [INFO] Running command: cat /var/lib/cwl/stg9a04d908-eb03-4189-99a3-26b76decb812/OceanDNA-b20995.fa | prodigal -d OceanDNA-b20995/cds.fna -a OceanDNA-b20995/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:32:21,509] [INFO] Task succeeded: Prodigal
[2023-03-18 08:32:21,509] [INFO] Task started: HMMsearch
[2023-03-18 08:32:21,509] [INFO] Running command: hmmsearch --tblout OceanDNA-b20995/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2856fde7-2c38-4c66-bb29-dc852d325d65/dqc_reference/reference_markers.hmm OceanDNA-b20995/protein.faa > /dev/null
[2023-03-18 08:32:21,756] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:32:21,757] [INFO] Found 6/6 markers.
[2023-03-18 08:32:21,788] [INFO] Query marker FASTA was written to OceanDNA-b20995/markers.fasta
[2023-03-18 08:32:21,788] [INFO] Task started: Blastn
[2023-03-18 08:32:21,789] [INFO] Running command: blastn -query OceanDNA-b20995/markers.fasta -db /var/lib/cwl/stg2856fde7-2c38-4c66-bb29-dc852d325d65/dqc_reference/reference_markers.fasta -out OceanDNA-b20995/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:32:22,411] [INFO] Task succeeded: Blastn
[2023-03-18 08:32:22,412] [INFO] Selected 44 target genomes.
[2023-03-18 08:32:22,412] [INFO] Target genome list was writen to OceanDNA-b20995/target_genomes.txt
[2023-03-18 08:32:22,434] [INFO] Task started: fastANI
[2023-03-18 08:32:22,434] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a04d908-eb03-4189-99a3-26b76decb812/OceanDNA-b20995.fa --refList OceanDNA-b20995/target_genomes.txt --output OceanDNA-b20995/fastani_result.tsv --threads 1
[2023-03-18 08:32:53,398] [INFO] Task succeeded: fastANI
[2023-03-18 08:32:53,399] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2856fde7-2c38-4c66-bb29-dc852d325d65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:32:53,399] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2856fde7-2c38-4c66-bb29-dc852d325d65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:32:53,413] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:32:53,413] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 08:32:53,413] [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
Arenimonas composti	strain=TR7-09	GCA_000747175.1	370776	370776	type	True	75.0077	92	1239	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	74.9889	95	1239	95	below_threshold
Luteimonas wenzhouensis	strain=YD-1	GCA_007859305.1	2599615	2599615	type	True	74.9448	66	1239	95	below_threshold
Massilia solisilvae	strain=JCM 31607	GCA_024753215.1	1811225	1811225	type	True	74.8658	52	1239	95	below_threshold
Corallococcus llansteffanensis	strain=CA051B	GCA_003612055.1	2316731	2316731	type	True	74.8475	74	1239	95	below_threshold
Corallococcus terminator	strain=CA054A	GCA_003611635.1	2316733	2316733	type	True	74.8445	64	1239	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	74.7949	92	1239	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_003258805.1	29408	29408	type	True	74.7938	84	1239	95	below_threshold
Pseudomonas sagittaria	strain=JCM 18195	GCA_900115715.1	1135990	1135990	type	True	74.7887	66	1239	95	below_threshold
Massilia terrae	strain=JCM 31606	GCA_024753145.1	1811224	1811224	type	True	74.7876	68	1239	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	74.7807	88	1239	95	below_threshold
Rhodoplanes elegans	strain=DSM 11907	GCA_016653355.1	29408	29408	type	True	74.7725	102	1239	95	below_threshold
Nocardiopsis coralli	strain=HNM0947	GCA_014892575.1	2772213	2772213	type	True	74.7724	71	1239	95	below_threshold
Arenimonas malthae	strain=CC-JY-1	GCA_000747075.1	354197	354197	type	True	74.7609	63	1239	95	below_threshold
Glycomyces artemisiae	strain=CGMCC 4.7067	GCA_003002955.1	1076443	1076443	type	True	74.7462	110	1239	95	below_threshold
Pseudomonas carbonaria	strain=CIP 111764	GCA_904061905.1	2762745	2762745	type	True	74.7429	56	1239	95	below_threshold
Caulobacter soli	strain=Ji-3-8	GCA_011045195.1	2708539	2708539	type	True	74.7383	76	1239	95	below_threshold
Caulobacter rhizosphaerae	strain=CGMCC 1.15915	GCA_014645055.1	2010972	2010972	type	True	74.7255	78	1239	95	below_threshold
Caulobacter rhizosphaerae	strain=KCTC 52515	GCA_010977555.1	2010972	2010972	type	True	74.7223	80	1239	95	below_threshold
Malikia granosa	strain=P1	GCA_002980595.1	263067	263067	type	True	74.7115	53	1239	95	below_threshold
Corallococcus praedator	strain=CA031B	GCA_003612125.1	2316724	2316724	type	True	74.7068	74	1239	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	74.692	107	1239	95	below_threshold
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	74.6756	85	1239	95	below_threshold
Glycomyces sambucus	strain=CGMCC 4.3147	GCA_900102815.1	380244	380244	type	True	74.655	98	1239	95	below_threshold
Glycomyces terrestris	strain=YIM 121974	GCA_003933745.1	2493553	2493553	type	True	74.645	107	1239	95	below_threshold
Cellulomonas massiliensis	strain=JC225	GCA_000312005.1	1465811	1465811	type	True	74.6427	90	1239	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 08:32:53,704] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20995/tc_result.tsv
[2023-03-18 08:32:53,705] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:32:53,705] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:32:53,705] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2856fde7-2c38-4c66-bb29-dc852d325d65/dqc_reference/checkm_data
[2023-03-18 08:32:53,706] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:32:53,715] [INFO] Task started: CheckM
[2023-03-18 08:32:53,715] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20995/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20995/checkm_input OceanDNA-b20995/checkm_result
[2023-03-18 08:33:52,771] [INFO] Task succeeded: CheckM
[2023-03-18 08:33:52,771] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.80%
Contamintation: 6.25%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-03-18 08:33:52,775] [INFO] ===== Completeness check finished =====
[2023-03-18 08:33:52,775] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:33:52,775] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20995/markers.fasta)
[2023-03-18 08:33:52,775] [INFO] Task started: Blastn
[2023-03-18 08:33:52,775] [INFO] Running command: blastn -query OceanDNA-b20995/markers.fasta -db /var/lib/cwl/stg2856fde7-2c38-4c66-bb29-dc852d325d65/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20995/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:33:53,789] [INFO] Task succeeded: Blastn
[2023-03-18 08:33:53,790] [INFO] Selected 47 target genomes.
[2023-03-18 08:33:53,790] [INFO] Target genome list was writen to OceanDNA-b20995/target_genomes_gtdb.txt
[2023-03-18 08:33:54,044] [INFO] Task started: fastANI
[2023-03-18 08:33:54,044] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a04d908-eb03-4189-99a3-26b76decb812/OceanDNA-b20995.fa --refList OceanDNA-b20995/target_genomes_gtdb.txt --output OceanDNA-b20995/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:34:31,500] [INFO] Task succeeded: fastANI
[2023-03-18 08:34:31,518] [INFO] Found 33 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:34:31,518] [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_903955385.1	s__CAJBNH01 sp903955385	75.9222	159	1239	d__Bacteria;p__Myxococcota;c__UBA9042;o__UBA9042;f__UBA9042;g__CAJBNH01	95.0	99.88	99.77	0.96	0.95	7	-
GCA_903917305.1	s__CAIXAA01 sp903917305	75.8609	154	1239	d__Bacteria;p__Myxococcota;c__UBA9042;o__UBA9042;f__UBA9042;g__CAIXAA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875335.1	s__SXRM01 sp016875335	75.8135	194	1239	d__Bacteria;p__Myxococcota;c__UBA9042;o__UBA9042;f__UBA9042;g__SXRM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016218865.1	s__SXRM01 sp016218865	75.7667	152	1239	d__Bacteria;p__Myxococcota;c__UBA9042;o__UBA9042;f__UBA9042;g__SXRM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903919145.1	s__SXRM01 sp903919145	75.724	157	1239	d__Bacteria;p__Myxococcota;c__UBA9042;o__UBA9042;f__UBA9042;g__SXRM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903869075.1	s__CAIYBN01 sp903869075	75.6636	168	1239	d__Bacteria;p__Myxococcota;c__UBA9042;o__UBA9042;f__UBA9042;g__CAIYBN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009692425.1	s__SHZF01 sp009692425	75.5825	154	1239	d__Bacteria;p__Myxococcota;c__UBA9042;o__UBA9042;f__UBA9042;g__SHZF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903929795.1	s__CAIYBN01 sp903929795	75.5784	138	1239	d__Bacteria;p__Myxococcota;c__UBA9042;o__UBA9042;f__UBA9042;g__CAIYBN01	95.0	99.55	99.37	0.95	0.92	7	-
GCA_006226565.1	s__PHBI01 sp006226565	75.247	212	1239	d__Bacteria;p__Myxococcota;c__UBA9042;o__PHBI01;f__PHBI01;g__PHBI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003695625.1	s__J065 sp003695625	75.1466	70	1239	d__Bacteria;p__Acidobacteriota;c__Mor1;o__J045;f__J045;g__J065	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011526585.1	s__WYBB01 sp011526585	75.0923	177	1239	d__Bacteria;p__Myxococcota;c__UBA9042;o__PHBI01;f__PHBI01;g__WYBB01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426365.1	s__Arenimonas composti	75.0046	92	1239	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	99.98	99.98	1.00	1.00	2	-
GCA_016703535.1	s__JADJBV01 sp016703535	74.9474	69	1239	d__Bacteria;p__Myxococcota;c__WYAZ01;o__WYAZ01;f__WYAZ01;g__JADJBV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002297645.1	s__Dokdonella_A sp002297645	74.8797	69	1239	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	99.81	99.81	0.89	0.89	2	-
GCF_006517175.1	s__Persicimonas caeni	74.8625	90	1239	d__Bacteria;p__Myxococcota;c__Bradymonadia;o__Bradymonadales;f__Bradymonadaceae;g__Persicimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016717005.1	s__UBA2376 sp016717005	74.8605	286	1239	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012933655.1	s__Myxococcus fallax	74.8543	91	1239	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202825.1	s__Chiayiivirga flava	74.8482	66	1239	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Chiayiivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014879745.1	s__CAIKUF01 sp014879745	74.812	77	1239	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAIKUF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000372525.1	s__Cupriavidus neocaledonicus	74.7961	87	1239	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Cupriavidus	95.0	99.97	99.97	0.99	0.98	3	-
GCF_014892575.1	s__Nocardiopsis coralli	74.7769	70	1239	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000747075.1	s__Arenimonas malthae	74.7637	61	1239	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Arenimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005144585.1	s__Polyangium fumosum	74.7486	156	1239	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Polyangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002955.1	s__Glycomyces artemisiae	74.7454	108	1239	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	97.80	97.80	0.92	0.92	2	-
GCA_016720545.1	s__JAAFHV01 sp016720545	74.7411	128	1239	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JAAFHV01	95.0	99.45	99.45	0.94	0.94	2	-
GCF_010977555.1	s__Caulobacter rhizosphaerae	74.7181	81	1239	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	98.18	95.88	0.94	0.91	4	-
GCA_016716715.1	s__Fen-183 sp016716715	74.7126	72	1239	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5066;f__UBA5066;g__Fen-183	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712525.1	s__JAAFHV01 sp016712525	74.7082	93	1239	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__JAAFHV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713325.1	s__OLB15 sp016713325	74.7004	51	1239	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__OLB15	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382345.1	s__Massilia niastensis	74.6677	68	1239	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102815.1	s__Glycomyces sambucus	74.6544	98	1239	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003933745.1	s__Glycomyces terrestris	74.6467	106	1239	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000312005.1	s__Cellulomonas massiliensis	74.6403	90	1239	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-03-18 08:34:31,518] [INFO] GTDB search result was written to OceanDNA-b20995/result_gtdb.tsv
[2023-03-18 08:34:31,519] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:34:31,521] [INFO] DFAST_QC result json was written to OceanDNA-b20995/dqc_result.json
[2023-03-18 08:34:31,521] [INFO] DFAST_QC completed!
[2023-03-18 08:34:31,522] [INFO] Total running time: 0h2m35s