[2023-03-18 23:27:53,725] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:27:53,735] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:27:53,735] [INFO] DQC Reference Directory: /var/lib/cwl/stg98424508-b3da-457f-94a0-51ba366ab769/dqc_reference
[2023-03-18 23:27:55,546] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:27:55,546] [INFO] Task started: Prodigal
[2023-03-18 23:27:55,546] [INFO] Running command: cat /var/lib/cwl/stg7a265bcb-54ad-4c2b-968b-da0bcdc798bf/OceanDNA-b30971.fa | prodigal -d OceanDNA-b30971/cds.fna -a OceanDNA-b30971/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:28:18,888] [INFO] Task succeeded: Prodigal
[2023-03-18 23:28:18,888] [INFO] Task started: HMMsearch
[2023-03-18 23:28:18,888] [INFO] Running command: hmmsearch --tblout OceanDNA-b30971/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg98424508-b3da-457f-94a0-51ba366ab769/dqc_reference/reference_markers.hmm OceanDNA-b30971/protein.faa > /dev/null
[2023-03-18 23:28:19,120] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:28:19,120] [INFO] Found 6/6 markers.
[2023-03-18 23:28:19,143] [INFO] Query marker FASTA was written to OceanDNA-b30971/markers.fasta
[2023-03-18 23:28:19,144] [INFO] Task started: Blastn
[2023-03-18 23:28:19,144] [INFO] Running command: blastn -query OceanDNA-b30971/markers.fasta -db /var/lib/cwl/stg98424508-b3da-457f-94a0-51ba366ab769/dqc_reference/reference_markers.fasta -out OceanDNA-b30971/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:28:20,085] [INFO] Task succeeded: Blastn
[2023-03-18 23:28:20,085] [INFO] Selected 32 target genomes.
[2023-03-18 23:28:20,086] [INFO] Target genome list was writen to OceanDNA-b30971/target_genomes.txt
[2023-03-18 23:28:20,107] [INFO] Task started: fastANI
[2023-03-18 23:28:20,107] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a265bcb-54ad-4c2b-968b-da0bcdc798bf/OceanDNA-b30971.fa --refList OceanDNA-b30971/target_genomes.txt --output OceanDNA-b30971/fastani_result.tsv --threads 1
[2023-03-18 23:28:47,096] [INFO] Task succeeded: fastANI
[2023-03-18 23:28:47,097] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg98424508-b3da-457f-94a0-51ba366ab769/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:28:47,097] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg98424508-b3da-457f-94a0-51ba366ab769/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:28:47,114] [INFO] Found 32 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:28:47,114] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 23:28:47,114] [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
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	77.0053	292	1235	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	77.0022	206	1235	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.8629	290	1235	95	below_threshold
Caenispirillum salinarum	strain=AK4	GCA_000315795.1	859058	859058	type	True	76.8095	274	1235	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.7876	304	1235	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.7799	309	1235	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.745	237	1235	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.667	199	1235	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	76.6557	194	1235	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	76.6511	200	1235	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	76.6327	203	1235	95	below_threshold
Magnetospirillum kuznetsovii	strain=LBB-42	GCA_003284725.1	2053833	2053833	type	True	76.6068	193	1235	95	below_threshold
Azospirillum thiophilum	strain=BV-S	GCA_001305595.1	528244	528244	type	True	76.5467	262	1235	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	76.5446	261	1235	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	76.4677	237	1235	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	76.4554	231	1235	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	76.4466	231	1235	95	below_threshold
Skermanella rosea	strain=KEMB 2255-458	GCA_016806835.2	1817965	1817965	type	True	76.4122	275	1235	95	below_threshold
Microvirga guangxiensis	strain=CGMCC 1.7666	GCA_900102135.1	549386	549386	type	True	76.4002	92	1235	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_003119195.2	1064539	1064539	type	True	76.3827	261	1235	95	below_threshold
Microvirga thermotolerans	strain=HR1	GCA_009363855.1	2651334	2651334	type	True	76.3603	122	1235	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_000237365.1	1064539	1064539	type	True	76.3296	266	1235	95	below_threshold
Magnetospirillum magnetotacticum	strain=MS-1	GCA_000829825.1	188	188	type	True	76.2771	166	1235	95	below_threshold
Stappia taiwanensis	strain=CCM 7757	GCA_014635285.1	992267	992267	type	True	76.2413	131	1235	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	76.233	176	1235	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.1384	226	1235	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	76.0587	161	1235	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.0313	191	1235	95	below_threshold
Caulobacter soli	strain=Ji-3-8	GCA_011045195.1	2708539	2708539	type	True	76.0038	181	1235	95	below_threshold
Tistrella bauzanensis	strain=CGMCC 1.10188	GCA_014636235.1	657419	657419	type	True	75.8728	157	1235	95	below_threshold
Methylobacterium goesingense	strain=DSM 21331	GCA_022179225.1	243690	243690	type	True	75.8302	135	1235	95	below_threshold
Aureimonas pseudogalii	strain=DSM 102238	GCA_014196835.1	1744844	1744844	type	True	75.8262	116	1235	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 23:28:47,115] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30971/tc_result.tsv
[2023-03-18 23:28:47,115] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:28:47,115] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:28:47,115] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg98424508-b3da-457f-94a0-51ba366ab769/dqc_reference/checkm_data
[2023-03-18 23:28:47,116] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:28:47,182] [INFO] Task started: CheckM
[2023-03-18 23:28:47,182] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30971/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30971/checkm_input OceanDNA-b30971/checkm_result
[2023-03-18 23:29:44,045] [INFO] Task succeeded: CheckM
[2023-03-18 23:29:44,046] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:29:44,048] [INFO] ===== Completeness check finished =====
[2023-03-18 23:29:44,048] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:29:44,048] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30971/markers.fasta)
[2023-03-18 23:29:44,049] [INFO] Task started: Blastn
[2023-03-18 23:29:44,049] [INFO] Running command: blastn -query OceanDNA-b30971/markers.fasta -db /var/lib/cwl/stg98424508-b3da-457f-94a0-51ba366ab769/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30971/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:29:45,954] [INFO] Task succeeded: Blastn
[2023-03-18 23:29:45,955] [INFO] Selected 12 target genomes.
[2023-03-18 23:29:45,955] [INFO] Target genome list was writen to OceanDNA-b30971/target_genomes_gtdb.txt
[2023-03-18 23:29:45,966] [INFO] Task started: fastANI
[2023-03-18 23:29:45,966] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a265bcb-54ad-4c2b-968b-da0bcdc798bf/OceanDNA-b30971.fa --refList OceanDNA-b30971/target_genomes_gtdb.txt --output OceanDNA-b30971/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:29:54,816] [INFO] Task succeeded: fastANI
[2023-03-18 23:29:54,823] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 23:29:54,824] [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_002325375.1	s__UBA1479 sp002325375	86.4257	1006	1235	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	85.457	876	1235	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_002781745.1	s__UBA1479 sp002781745	84.8179	872	1235	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_002696205.1	s__UBA1479 sp002696205	82.3496	738	1235	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	81.2129	737	1235	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_017640505.1	s__UBA4479 sp017640505	77.241	259	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA4479	95.0	99.97	99.97	1.00	1.00	2	-
GCA_014382345.1	s__Casp-alpha2 sp014382345	77.0201	228	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.86	99.86	0.92	0.92	2	-
GCF_001650715.1	s__Phaeospirillum marisnigri	76.6443	195	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000171835.1	s__Thalassobaculum_A sp000171835	76.3961	172	1235	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_014380005.1	s__Magnetospirillum sp014380005	76.3582	159	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007694935.1	s__REEP01 sp007694935	76.2885	124	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__REEP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762225.1	s__Pseudochelatococcus lubricantis	75.7227	119	1235	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Pseudochelatococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:29:54,824] [INFO] GTDB search result was written to OceanDNA-b30971/result_gtdb.tsv
[2023-03-18 23:29:54,824] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:29:54,826] [INFO] DFAST_QC result json was written to OceanDNA-b30971/dqc_result.json
[2023-03-18 23:29:54,826] [INFO] DFAST_QC completed!
[2023-03-18 23:29:54,826] [INFO] Total running time: 0h2m1s