[2023-03-15 22:23:01,937] [INFO] DFAST_QC pipeline started.
[2023-03-15 22:23:01,947] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 22:23:01,947] [INFO] DQC Reference Directory: /var/lib/cwl/stg6bced1a8-ebb3-4954-b652-206d554353c3/dqc_reference
[2023-03-15 22:23:03,675] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 22:23:03,676] [INFO] Task started: Prodigal
[2023-03-15 22:23:03,676] [INFO] Running command: cat /var/lib/cwl/stgc944f7b5-ca55-4781-8925-afd78a51e05b/OceanDNA-b32599.fa | prodigal -d OceanDNA-b32599/cds.fna -a OceanDNA-b32599/protein.faa -g 11 -q > /dev/null
[2023-03-15 22:23:20,264] [INFO] Task succeeded: Prodigal
[2023-03-15 22:23:20,265] [INFO] Task started: HMMsearch
[2023-03-15 22:23:20,265] [INFO] Running command: hmmsearch --tblout OceanDNA-b32599/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6bced1a8-ebb3-4954-b652-206d554353c3/dqc_reference/reference_markers.hmm OceanDNA-b32599/protein.faa > /dev/null
[2023-03-15 22:23:20,461] [INFO] Task succeeded: HMMsearch
[2023-03-15 22:23:20,461] [INFO] Found 6/6 markers.
[2023-03-15 22:23:20,486] [INFO] Query marker FASTA was written to OceanDNA-b32599/markers.fasta
[2023-03-15 22:23:20,487] [INFO] Task started: Blastn
[2023-03-15 22:23:20,487] [INFO] Running command: blastn -query OceanDNA-b32599/markers.fasta -db /var/lib/cwl/stg6bced1a8-ebb3-4954-b652-206d554353c3/dqc_reference/reference_markers.fasta -out OceanDNA-b32599/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:23:21,274] [INFO] Task succeeded: Blastn
[2023-03-15 22:23:21,274] [INFO] Selected 28 target genomes.
[2023-03-15 22:23:21,275] [INFO] Target genome list was writen to OceanDNA-b32599/target_genomes.txt
[2023-03-15 22:23:21,309] [INFO] Task started: fastANI
[2023-03-15 22:23:21,309] [INFO] Running command: fastANI --query /var/lib/cwl/stgc944f7b5-ca55-4781-8925-afd78a51e05b/OceanDNA-b32599.fa --refList OceanDNA-b32599/target_genomes.txt --output OceanDNA-b32599/fastani_result.tsv --threads 1
[2023-03-15 22:23:41,857] [INFO] Task succeeded: fastANI
[2023-03-15 22:23:41,857] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6bced1a8-ebb3-4954-b652-206d554353c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 22:23:41,857] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6bced1a8-ebb3-4954-b652-206d554353c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 22:23:41,873] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 22:23:41,873] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 22:23:41,873] [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
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	78.3332	322	849	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	77.0635	144	849	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	77.0233	109	849	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.9616	121	849	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	76.8381	125	849	95	below_threshold
Nisaea nitritireducens	strain=DSM 19540	GCA_014904795.1	568392	568392	type	True	76.7489	129	849	95	below_threshold
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	76.4534	101	849	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.3848	135	849	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	76.3806	107	849	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.3632	135	849	95	below_threshold
Azospirillum palustre	strain=B2	GCA_002573965.1	2044885	2044885	type	True	76.238	106	849	95	below_threshold
Azospirillum melinis	strain=TMCY 0552	GCA_017876055.1	328839	328839	type	True	76.183	98	849	95	below_threshold
Roseospira navarrensis	strain=DSM 15114	GCA_009601025.1	140058	140058	type	True	76.1561	73	849	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	76.145	55	849	95	below_threshold
Methylorubrum suomiense	strain=DSM 14458	GCA_022179765.1	144191	144191	type	True	76.1444	51	849	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	76.0852	89	849	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.0004	77	849	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	75.9635	119	849	95	below_threshold
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	75.9374	50	849	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	75.7745	69	849	95	below_threshold
Roseomonas mucosa	strain=ATCC BAA-692	GCA_000622225.1	207340	207340	type	True	75.7255	60	849	95	below_threshold
Azospirillum griseum	strain=L-25-5 w-1	GCA_003966125.1	2496639	2496639	type	True	75.7064	75	849	95	below_threshold
Acuticoccus yangtzensis	strain=JL1095	GCA_003073145.1	1443441	1443441	type	True	75.5998	63	849	95	below_threshold
Acuticoccus yangtzensis	strain=JL1095	GCA_001927245.1	1443441	1443441	type	True	75.5816	64	849	95	below_threshold
Roseomonas gilardii subsp. rosea	strain=NCTC13290	GCA_900455865.1	243956	257708	type	True	75.5441	60	849	95	below_threshold
Roseomonas gilardii subsp. rosea	strain=ATCC BAA-691	GCA_000518625.1	243956	257708	type	True	75.5094	63	849	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	75.4108	75	849	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	75.2631	51	849	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 22:23:41,873] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32599/tc_result.tsv
[2023-03-15 22:23:41,873] [INFO] ===== Taxonomy check completed =====
[2023-03-15 22:23:41,873] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 22:23:41,873] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6bced1a8-ebb3-4954-b652-206d554353c3/dqc_reference/checkm_data
[2023-03-15 22:23:41,874] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 22:23:41,879] [INFO] Task started: CheckM
[2023-03-15 22:23:41,879] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32599/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32599/checkm_input OceanDNA-b32599/checkm_result
[2023-03-15 22:24:25,717] [INFO] Task succeeded: CheckM
[2023-03-15 22:24:25,718] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.41%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 22:24:25,721] [INFO] ===== Completeness check finished =====
[2023-03-15 22:24:25,721] [INFO] ===== Start GTDB Search =====
[2023-03-15 22:24:25,721] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32599/markers.fasta)
[2023-03-15 22:24:25,722] [INFO] Task started: Blastn
[2023-03-15 22:24:25,723] [INFO] Running command: blastn -query OceanDNA-b32599/markers.fasta -db /var/lib/cwl/stg6bced1a8-ebb3-4954-b652-206d554353c3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32599/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:24:27,130] [INFO] Task succeeded: Blastn
[2023-03-15 22:24:27,131] [INFO] Selected 19 target genomes.
[2023-03-15 22:24:27,131] [INFO] Target genome list was writen to OceanDNA-b32599/target_genomes_gtdb.txt
[2023-03-15 22:24:27,142] [INFO] Task started: fastANI
[2023-03-15 22:24:27,142] [INFO] Running command: fastANI --query /var/lib/cwl/stgc944f7b5-ca55-4781-8925-afd78a51e05b/OceanDNA-b32599.fa --refList OceanDNA-b32599/target_genomes_gtdb.txt --output OceanDNA-b32599/fastani_result_gtdb.tsv --threads 1
[2023-03-15 22:24:42,535] [INFO] Task succeeded: fastANI
[2023-03-15 22:24:42,545] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 22:24:42,545] [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
GCF_900102465.1	s__Thalassobaculum litoreum	78.493	356	849	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum	95.0	98.83	98.83	0.96	0.96	2	-
GCF_014652915.1	s__Thalassobaculum_A fulvum	78.3332	322	849	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401495.1	s__Thalassobaculum_A sp018401495	77.9957	278	849	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000171835.1	s__Thalassobaculum_A sp000171835	77.9054	254	849	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013203465.1	s__JABMNR01 sp013203465	77.7445	248	849	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__JABMNR01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904795.1	s__Nisaea nitritireducens	76.7489	129	849	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008843145.1	s__Skermanella pratensis	76.4523	101	849	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	76.3497	136	849	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_009789575.1	s__Stappia indica_A	76.2953	84	849	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016765655.1	s__Skermanella mucosa	76.2536	120	849	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000264455.2	s__Tistrella mobilis	76.0225	106	849	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Tistrellales;f__Tistrellaceae;g__Tistrella	95.0	96.38	95.97	0.88	0.84	5	-
GCF_000342045.1	s__Phaeospirillum caucaseum	76.0004	77	849	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000829825.1	s__Phaeospirillum magnetotacticum	75.9089	57	849	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016107285.1	s__Roseomonas sp016107285	75.8544	76	849	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622225.1	s__Roseomonas mucosa	75.7255	60	849	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	99.41	98.67	0.95	0.89	8	-
GCF_001941945.1	s__Roseomonas gilardii	75.6797	68	849	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	96.77	95.72	0.89	0.83	6	-
GCF_001927245.1	s__Acuticoccus yangtzensis	75.5989	63	849	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Amorphaceae;g__Acuticoccus	95.0	98.76	97.53	0.97	0.95	3	-
GCA_016195115.1	s__JACQAI01 sp016195115	75.5477	66	849	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Elsterales;f__Elsteraceae;g__JACQAI01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 22:24:42,546] [INFO] GTDB search result was written to OceanDNA-b32599/result_gtdb.tsv
[2023-03-15 22:24:42,546] [INFO] ===== GTDB Search completed =====
[2023-03-15 22:24:42,548] [INFO] DFAST_QC result json was written to OceanDNA-b32599/dqc_result.json
[2023-03-15 22:24:42,548] [INFO] DFAST_QC completed!
[2023-03-15 22:24:42,548] [INFO] Total running time: 0h1m41s