[2023-03-18 02:48:47,727] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:48:47,727] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:48:47,727] [INFO] DQC Reference Directory: /var/lib/cwl/stg759bcc1c-7d28-47d8-a10e-39d9da3247a9/dqc_reference
[2023-03-18 02:48:49,545] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:48:49,545] [INFO] Task started: Prodigal
[2023-03-18 02:48:49,546] [INFO] Running command: cat /var/lib/cwl/stg848fb0ba-0afd-4ede-ab9f-2953a2227e39/OceanDNA-b37266.fa | prodigal -d OceanDNA-b37266/cds.fna -a OceanDNA-b37266/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:49:17,344] [INFO] Task succeeded: Prodigal
[2023-03-18 02:49:17,345] [INFO] Task started: HMMsearch
[2023-03-18 02:49:17,345] [INFO] Running command: hmmsearch --tblout OceanDNA-b37266/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg759bcc1c-7d28-47d8-a10e-39d9da3247a9/dqc_reference/reference_markers.hmm OceanDNA-b37266/protein.faa > /dev/null
[2023-03-18 02:49:17,619] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:49:17,620] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg848fb0ba-0afd-4ede-ab9f-2953a2227e39/OceanDNA-b37266.fa]
[2023-03-18 02:49:17,648] [INFO] Query marker FASTA was written to OceanDNA-b37266/markers.fasta
[2023-03-18 02:49:17,649] [INFO] Task started: Blastn
[2023-03-18 02:49:17,650] [INFO] Running command: blastn -query OceanDNA-b37266/markers.fasta -db /var/lib/cwl/stg759bcc1c-7d28-47d8-a10e-39d9da3247a9/dqc_reference/reference_markers.fasta -out OceanDNA-b37266/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:49:18,520] [INFO] Task succeeded: Blastn
[2023-03-18 02:49:18,521] [INFO] Selected 30 target genomes.
[2023-03-18 02:49:18,521] [INFO] Target genome list was writen to OceanDNA-b37266/target_genomes.txt
[2023-03-18 02:49:18,582] [INFO] Task started: fastANI
[2023-03-18 02:49:18,582] [INFO] Running command: fastANI --query /var/lib/cwl/stg848fb0ba-0afd-4ede-ab9f-2953a2227e39/OceanDNA-b37266.fa --refList OceanDNA-b37266/target_genomes.txt --output OceanDNA-b37266/fastani_result.tsv --threads 1
[2023-03-18 02:49:41,749] [INFO] Task succeeded: fastANI
[2023-03-18 02:49:41,749] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg759bcc1c-7d28-47d8-a10e-39d9da3247a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:49:41,750] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg759bcc1c-7d28-47d8-a10e-39d9da3247a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:49:41,766] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:49:41,766] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 02:49:41,766] [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
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	76.5442	196	1524	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	76.502	206	1524	95	below_threshold
Pseudomonas linyingensis	strain=LMG 25967	GCA_900109175.1	915471	915471	type	True	76.4929	243	1524	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	76.4583	248	1524	95	below_threshold
Alcanivorax profundimaris	strain=ST75FaO-1	GCA_015265435.1	2735259	2735259	type	True	76.3584	252	1524	95	below_threshold
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	76.3372	310	1524	95	below_threshold
Pseudomonas oryzihabitans	strain=NBRC 102199	GCA_000730625.1	47885	47885	suspected-type	True	76.3362	202	1524	95	below_threshold
Pseudomonas oryzihabitans	strain=DSM 6835	GCA_012986195.1	47885	47885	suspected-type	True	76.3328	200	1524	95	below_threshold
Halomonas lactosivorans	strain=KCTC 52281	GCA_003254665.1	2185141	2185141	type	True	76.3235	224	1524	95	below_threshold
Halomonas stenophila	strain=CECT 7744	GCA_014192275.1	795312	795312	type	True	76.2985	214	1524	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	76.295	233	1524	95	below_threshold
Pseudomonas delhiensis	strain=CCM 7361	GCA_900099945.1	366289	366289	type	True	76.2931	347	1524	95	below_threshold
Pseudomonas citronellolis	strain=LMG 18378	GCA_900112375.1	53408	53408	type	True	76.29	329	1524	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	76.2883	333	1524	95	below_threshold
Pseudomonas delhiensis	strain=RLD-1	GCA_900187975.1	366289	366289	type	True	76.2662	349	1524	95	below_threshold
Halomonas zhangzhouensis	strain=MCCC 1A11036	GCA_021404465.1	2733481	2733481	type	True	76.2646	139	1524	95	below_threshold
Pseudomonas psychrotolerans	strain=DSM 15758	GCA_900102665.1	237610	237610	suspected-type	True	76.2552	211	1524	95	below_threshold
Pseudomonas psychrotolerans	strain=DSM 15758	GCA_012985915.1	237610	237610	suspected-type	True	76.2396	210	1524	95	below_threshold
Pseudomonas mangrovi	strain=TC11	GCA_003052585.1	2161748	2161748	type	True	76.2194	160	1524	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_001042925.1	287	287	type	True	76.1614	248	1524	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_012987025.1	287	287	type	True	76.1612	248	1524	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_900167195.1	287	287	type	True	76.1612	251	1524	95	below_threshold
Pseudomonas aeruginosa	strain=NCTC10332	GCA_001457615.1	287	287	type	True	76.1215	254	1524	95	below_threshold
Seongchinamella sediminis	strain=U0301	GCA_003457605.1	2283635	2283635	type	True	76.0059	130	1524	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	75.9325	184	1524	95	below_threshold
Alcanivorax limicola	strain=JB21	GCA_019931215.1	2874102	2874102	type	True	75.9172	71	1524	95	below_threshold
Saccharospirillum salsuginis	strain=KCTC 22169	GCA_014651855.1	418750	418750	type	True	75.8153	87	1524	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	75.7342	191	1524	95	below_threshold
Halotalea alkalilenta	strain=DSM 17697	GCA_000621205.1	376489	376489	type	True	75.6435	144	1524	95	below_threshold
Ralstonia pickettii	strain=ATCC 27511	GCA_000743455.1	329	329	type	True	75.5459	93	1524	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 02:49:41,766] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37266/tc_result.tsv
[2023-03-18 02:49:41,766] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:49:41,766] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:49:41,766] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg759bcc1c-7d28-47d8-a10e-39d9da3247a9/dqc_reference/checkm_data
[2023-03-18 02:49:41,767] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:49:41,772] [INFO] Task started: CheckM
[2023-03-18 02:49:41,773] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37266/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37266/checkm_input OceanDNA-b37266/checkm_result
[2023-03-18 02:50:55,914] [INFO] Task succeeded: CheckM
[2023-03-18 02:50:55,914] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.42%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 02:50:55,917] [INFO] ===== Completeness check finished =====
[2023-03-18 02:50:55,917] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:50:55,917] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37266/markers.fasta)
[2023-03-18 02:50:55,919] [INFO] Task started: Blastn
[2023-03-18 02:50:55,919] [INFO] Running command: blastn -query OceanDNA-b37266/markers.fasta -db /var/lib/cwl/stg759bcc1c-7d28-47d8-a10e-39d9da3247a9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37266/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:50:57,532] [INFO] Task succeeded: Blastn
[2023-03-18 02:50:57,533] [INFO] Selected 21 target genomes.
[2023-03-18 02:50:57,533] [INFO] Target genome list was writen to OceanDNA-b37266/target_genomes_gtdb.txt
[2023-03-18 02:50:57,653] [INFO] Task started: fastANI
[2023-03-18 02:50:57,654] [INFO] Running command: fastANI --query /var/lib/cwl/stg848fb0ba-0afd-4ede-ab9f-2953a2227e39/OceanDNA-b37266.fa --refList OceanDNA-b37266/target_genomes_gtdb.txt --output OceanDNA-b37266/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:51:12,374] [INFO] Task succeeded: fastANI
[2023-03-18 02:51:12,386] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 02:51:12,386] [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_002480525.1	s__UBA7803 sp002480525	99.7457	1210	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA7803	95.0	99.35	98.95	0.83	0.81	3	conclusive
GCA_003247835.1	s__SZUA-309 sp003247835	77.5395	331	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__SZUA-309	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009843635.1	s__UBA2168 sp009843635	77.1912	281	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA2168	95.0	97.76	96.95	0.89	0.86	7	-
GCA_002348385.1	s__UBA2965 sp002348385	76.9999	168	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA2965	95.0	98.25	98.25	0.91	0.91	2	-
GCA_007694905.1	s__SLTB01 sp007694905	76.5412	242	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__SLTB01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003056305.1	s__Halomonas denitrificans	76.4693	247	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003476445.1	s__UBA7803 sp003476445	76.3856	142	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA7803	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363755.1	s__Halomonas sp009363755	76.3797	241	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000730625.1	s__Pseudomonas_B oryzihabitans	76.3278	203	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_B	95.0	97.97	96.38	0.92	0.87	28	-
GCA_003248125.1	s__SZUA-521 sp003248125	76.3141	164	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__SZUA-521	95.0	99.60	99.60	0.84	0.84	2	-
GCF_014192275.1	s__Halomonas stenophila	76.2999	214	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007131295.1	s__SLTB01 sp007131295	76.2922	196	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__SLTB01	95.0	99.75	99.70	0.93	0.92	5	-
GCF_900187975.1	s__Pseudomonas delhiensis	76.2623	350	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.078	98.79	97.59	0.94	0.89	3	-
GCF_003052585.1	s__Pseudomonas_E mangrovi	76.2194	160	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002327525.1	s__UBA2168 sp002327525	76.1488	128	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA2168	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013519935.1	s__WFHF3C12 sp013519935	75.9436	171	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Nitrococcaceae;g__WFHF3C12	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007133445.1	s__Aquisalimonas sp007133445	75.9026	63	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Aquisalimonadaceae;g__Aquisalimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001785175.1	s__MFSY01 sp001785175	75.8311	91	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Acidiferrobacterales;f__Sulfurifustaceae;g__MFSY01	95.0	97.98	97.98	0.76	0.76	2	-
GCF_000559025.1	s__Luteimonas huabeiensis	75.7673	259	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240295.1	s__Plasticicumulans sp003962905	75.7612	201	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Competibacterales;f__Competibacteraceae;g__Plasticicumulans	95.0	98.50	98.50	0.84	0.84	2	-
GCF_013425525.1	s__Luteimonas sp013425525	75.7357	191	1524	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 02:51:12,386] [INFO] GTDB search result was written to OceanDNA-b37266/result_gtdb.tsv
[2023-03-18 02:51:12,386] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:51:12,389] [INFO] DFAST_QC result json was written to OceanDNA-b37266/dqc_result.json
[2023-03-18 02:51:12,389] [INFO] DFAST_QC completed!
[2023-03-18 02:51:12,389] [INFO] Total running time: 0h2m25s