[2023-03-15 07:03:38,900] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:03:38,900] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:03:38,900] [INFO] DQC Reference Directory: /var/lib/cwl/stg44f84948-e160-400d-be1f-be8162940980/dqc_reference
[2023-03-15 07:03:40,045] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:03:40,046] [INFO] Task started: Prodigal
[2023-03-15 07:03:40,046] [INFO] Running command: cat /var/lib/cwl/stga434f4b8-6e07-4af4-8842-fc33c0082914/OceanDNA-b30953.fa | prodigal -d OceanDNA-b30953/cds.fna -a OceanDNA-b30953/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:04:05,086] [INFO] Task succeeded: Prodigal
[2023-03-15 07:04:05,086] [INFO] Task started: HMMsearch
[2023-03-15 07:04:05,086] [INFO] Running command: hmmsearch --tblout OceanDNA-b30953/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44f84948-e160-400d-be1f-be8162940980/dqc_reference/reference_markers.hmm OceanDNA-b30953/protein.faa > /dev/null
[2023-03-15 07:04:05,303] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:04:05,304] [INFO] Found 6/6 markers.
[2023-03-15 07:04:05,364] [INFO] Query marker FASTA was written to OceanDNA-b30953/markers.fasta
[2023-03-15 07:04:05,365] [INFO] Task started: Blastn
[2023-03-15 07:04:05,365] [INFO] Running command: blastn -query OceanDNA-b30953/markers.fasta -db /var/lib/cwl/stg44f84948-e160-400d-be1f-be8162940980/dqc_reference/reference_markers.fasta -out OceanDNA-b30953/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:04:06,295] [INFO] Task succeeded: Blastn
[2023-03-15 07:04:06,299] [INFO] Selected 28 target genomes.
[2023-03-15 07:04:06,299] [INFO] Target genome list was writen to OceanDNA-b30953/target_genomes.txt
[2023-03-15 07:04:06,347] [INFO] Task started: fastANI
[2023-03-15 07:04:06,347] [INFO] Running command: fastANI --query /var/lib/cwl/stga434f4b8-6e07-4af4-8842-fc33c0082914/OceanDNA-b30953.fa --refList OceanDNA-b30953/target_genomes.txt --output OceanDNA-b30953/fastani_result.tsv --threads 1
[2023-03-15 07:04:30,935] [INFO] Task succeeded: fastANI
[2023-03-15 07:04:30,936] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44f84948-e160-400d-be1f-be8162940980/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:04:30,936] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44f84948-e160-400d-be1f-be8162940980/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:04:30,951] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:04:30,952] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 07:04:30,952] [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
Caenispirillum salinarum	strain=AK4	GCA_000315795.1	859058	859058	type	True	77.4677	352	1229	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	77.4584	376	1229	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	77.2241	258	1229	95	below_threshold
Azospirillum formosense	strain=CC-NFb-7	GCA_013340925.1	861533	861533	type	True	77.2062	303	1229	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	77.1125	324	1229	95	below_threshold
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	77.0864	380	1229	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	77.0845	313	1229	95	below_threshold
Magnetospirillum kuznetsovii	strain=LBB-42	GCA_003284725.1	2053833	2053833	type	True	77.0113	214	1229	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_008274945.1	192	192	type	True	77.0005	349	1229	95	below_threshold
Roseospirillum parvum	strain=930I	GCA_900100455.1	83401	83401	type	True	76.9828	282	1229	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_007827425.1	192	192	type	True	76.9822	349	1229	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	76.9474	343	1229	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	76.9468	311	1229	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	76.9388	312	1229	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	76.9361	381	1229	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.8957	245	1229	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	76.8868	229	1229	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	76.8816	251	1229	95	below_threshold
Azospirillum melinis	strain=TMCY 0552	GCA_017876055.1	328839	328839	type	True	76.7134	340	1229	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.6766	312	1229	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	76.568	89	1229	95	below_threshold
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	76.4183	292	1229	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	76.3163	260	1229	95	below_threshold
Rhodospirillum rubrum	strain=DSM 467	GCA_019134555.1	1085	1085	type	True	76.1472	224	1229	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	76.0922	223	1229	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	76.0448	224	1229	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	76.0011	272	1229	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	75.8731	254	1229	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 07:04:30,956] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30953/tc_result.tsv
[2023-03-15 07:04:30,962] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:04:30,962] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:04:30,962] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44f84948-e160-400d-be1f-be8162940980/dqc_reference/checkm_data
[2023-03-15 07:04:30,963] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:04:30,996] [INFO] Task started: CheckM
[2023-03-15 07:04:30,996] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30953/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30953/checkm_input OceanDNA-b30953/checkm_result
[2023-03-15 07:05:31,291] [INFO] Task succeeded: CheckM
[2023-03-15 07:05:31,292] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 07:05:31,321] [INFO] ===== Completeness check finished =====
[2023-03-15 07:05:31,322] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:05:31,322] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30953/markers.fasta)
[2023-03-15 07:05:31,323] [INFO] Task started: Blastn
[2023-03-15 07:05:31,323] [INFO] Running command: blastn -query OceanDNA-b30953/markers.fasta -db /var/lib/cwl/stg44f84948-e160-400d-be1f-be8162940980/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30953/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:05:33,174] [INFO] Task succeeded: Blastn
[2023-03-15 07:05:33,179] [INFO] Selected 13 target genomes.
[2023-03-15 07:05:33,179] [INFO] Target genome list was writen to OceanDNA-b30953/target_genomes_gtdb.txt
[2023-03-15 07:05:33,340] [INFO] Task started: fastANI
[2023-03-15 07:05:33,340] [INFO] Running command: fastANI --query /var/lib/cwl/stga434f4b8-6e07-4af4-8842-fc33c0082914/OceanDNA-b30953.fa --refList OceanDNA-b30953/target_genomes_gtdb.txt --output OceanDNA-b30953/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:05:44,114] [INFO] Task succeeded: fastANI
[2023-03-15 07:05:44,122] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 07:05:44,122] [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_002781745.1	s__UBA1479 sp002781745	82.4635	796	1229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002325375.1	s__UBA1479 sp002325375	81.162	840	1229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	99.20	96.43	0.95	0.85	6	-
GCA_002706405.1	s__UBA1479 sp002706405	80.9006	720	1229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	99.68	99.68	0.89	0.89	2	-
GCA_002696205.1	s__UBA1479 sp002696205	80.3069	648	1229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002433335.1	s__UBA1479 sp002433335	79.4333	579	1229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900230255.1	s__Caenispirillum bisanense	77.4651	419	1229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Caenispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872535.1	s__2-12-FULL-67-15 sp016872535	77.2125	254	1229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__2-12-FULL-67-15;g__2-12-FULL-67-15	95.0	95.80	95.80	0.86	0.86	2	-
GCA_017640505.1	s__UBA4479 sp017640505	77.1393	273	1229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA4479	95.0	99.97	99.97	1.00	1.00	2	-
GCF_000342045.1	s__Phaeospirillum caucaseum	77.1101	309	1229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000009985.1	s__Phaeospirillum magneticum	76.9734	293	1229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006738645.1	s__Stella humosa	76.9389	313	1229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003116015.1	s__Azospirillum sp003116015	76.8443	379	1229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576705.1	s__SYSU-D60015 sp003576705	76.6848	307	1229	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__SYSU-D60015	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 07:05:44,123] [INFO] GTDB search result was written to OceanDNA-b30953/result_gtdb.tsv
[2023-03-15 07:05:44,123] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:05:44,125] [INFO] DFAST_QC result json was written to OceanDNA-b30953/dqc_result.json
[2023-03-15 07:05:44,125] [INFO] DFAST_QC completed!
[2023-03-15 07:05:44,125] [INFO] Total running time: 0h2m5s