[2023-03-15 21:01:44,364] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:01:44,364] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:01:44,364] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4b03c4c-4f0a-41a1-94e3-87250bd3da0b/dqc_reference
[2023-03-15 21:01:45,597] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:01:45,597] [INFO] Task started: Prodigal
[2023-03-15 21:01:45,597] [INFO] Running command: cat /var/lib/cwl/stgac2691c4-0e37-4c32-81fa-cbc2520a9aaf/OceanDNA-b30955.fa | prodigal -d OceanDNA-b30955/cds.fna -a OceanDNA-b30955/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:02:03,352] [INFO] Task succeeded: Prodigal
[2023-03-15 21:02:03,352] [INFO] Task started: HMMsearch
[2023-03-15 21:02:03,352] [INFO] Running command: hmmsearch --tblout OceanDNA-b30955/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4b03c4c-4f0a-41a1-94e3-87250bd3da0b/dqc_reference/reference_markers.hmm OceanDNA-b30955/protein.faa > /dev/null
[2023-03-15 21:02:03,543] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:02:03,544] [INFO] Found 6/6 markers.
[2023-03-15 21:02:03,566] [INFO] Query marker FASTA was written to OceanDNA-b30955/markers.fasta
[2023-03-15 21:02:03,566] [INFO] Task started: Blastn
[2023-03-15 21:02:03,566] [INFO] Running command: blastn -query OceanDNA-b30955/markers.fasta -db /var/lib/cwl/stgf4b03c4c-4f0a-41a1-94e3-87250bd3da0b/dqc_reference/reference_markers.fasta -out OceanDNA-b30955/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:02:04,271] [INFO] Task succeeded: Blastn
[2023-03-15 21:02:04,271] [INFO] Selected 29 target genomes.
[2023-03-15 21:02:04,272] [INFO] Target genome list was writen to OceanDNA-b30955/target_genomes.txt
[2023-03-15 21:02:04,292] [INFO] Task started: fastANI
[2023-03-15 21:02:04,293] [INFO] Running command: fastANI --query /var/lib/cwl/stgac2691c4-0e37-4c32-81fa-cbc2520a9aaf/OceanDNA-b30955.fa --refList OceanDNA-b30955/target_genomes.txt --output OceanDNA-b30955/fastani_result.tsv --threads 1
[2023-03-15 21:02:28,785] [INFO] Task succeeded: fastANI
[2023-03-15 21:02:28,786] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4b03c4c-4f0a-41a1-94e3-87250bd3da0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:02:28,786] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4b03c4c-4f0a-41a1-94e3-87250bd3da0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:02:28,801] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:02:28,801] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 21:02:28,801] [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	76.5646	156	962	95	below_threshold
Roseospirillum parvum	strain=930I	GCA_900100455.1	83401	83401	type	True	76.2983	113	962	95	below_threshold
Azospirillum palustre	strain=B2	GCA_002573965.1	2044885	2044885	type	True	76.2094	163	962	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.2005	127	962	95	below_threshold
Azospirillum melinis	strain=TMCY 0552	GCA_017876055.1	328839	328839	type	True	76.1952	151	962	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	76.1913	127	962	95	below_threshold
Azospirillum melinis	strain=TMCY0552	GCA_013340935.1	328839	328839	type	True	76.1889	150	962	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.1558	188	962	95	below_threshold
Magnetospirillum kuznetsovii	strain=LBB-42	GCA_003284725.1	2053833	2053833	type	True	76.1538	117	962	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.1394	188	962	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	76.0712	145	962	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_000513295.1	55518	55518	type	True	76.0692	107	962	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	76.0627	153	962	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	76.0446	121	962	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	76.0221	106	962	95	below_threshold
Magnetospirillum gryphiswaldense	strain=MSR-1	GCA_002995515.1	55518	55518	type	True	76.0131	111	962	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	75.9891	117	962	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	75.9637	129	962	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	75.9617	59	962	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	75.9617	59	962	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	75.9222	100	962	95	below_threshold
Azospirillum griseum	strain=L-25-5 w-1	GCA_003966125.1	2496639	2496639	type	True	75.9155	128	962	95	below_threshold
Aminobacter aganoensis	strain=DSM 7051	GCA_014206975.1	83264	83264	type	True	75.8704	88	962	95	below_threshold
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	75.8624	141	962	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	75.7912	111	962	95	below_threshold
Nitrospirillum iridis	strain=DSM 22198	GCA_014205765.1	765888	765888	type	True	75.7227	113	962	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	75.5654	152	962	95	below_threshold
Mesorhizobium caraganae	strain=LMG 24397	GCA_016836705.1	483206	483206	type	True	75.5502	83	962	95	below_threshold
Mesorhizobium camelthorni	strain=CCNWXJ 40-4	GCA_011045125.1	475069	475069	type	True	75.4502	72	962	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 21:02:28,801] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30955/tc_result.tsv
[2023-03-15 21:02:28,802] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:02:28,802] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:02:28,802] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4b03c4c-4f0a-41a1-94e3-87250bd3da0b/dqc_reference/checkm_data
[2023-03-15 21:02:28,802] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:02:28,888] [INFO] Task started: CheckM
[2023-03-15 21:02:28,888] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30955/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30955/checkm_input OceanDNA-b30955/checkm_result
[2023-03-15 21:03:14,035] [INFO] Task succeeded: CheckM
[2023-03-15 21:03:14,036] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.11%
Contamintation: 2.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 21:03:14,038] [INFO] ===== Completeness check finished =====
[2023-03-15 21:03:14,038] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:03:14,038] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30955/markers.fasta)
[2023-03-15 21:03:14,038] [INFO] Task started: Blastn
[2023-03-15 21:03:14,038] [INFO] Running command: blastn -query OceanDNA-b30955/markers.fasta -db /var/lib/cwl/stgf4b03c4c-4f0a-41a1-94e3-87250bd3da0b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30955/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:03:15,310] [INFO] Task succeeded: Blastn
[2023-03-15 21:03:15,310] [INFO] Selected 10 target genomes.
[2023-03-15 21:03:15,310] [INFO] Target genome list was writen to OceanDNA-b30955/target_genomes_gtdb.txt
[2023-03-15 21:03:15,554] [INFO] Task started: fastANI
[2023-03-15 21:03:15,554] [INFO] Running command: fastANI --query /var/lib/cwl/stgac2691c4-0e37-4c32-81fa-cbc2520a9aaf/OceanDNA-b30955.fa --refList OceanDNA-b30955/target_genomes_gtdb.txt --output OceanDNA-b30955/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:03:24,087] [INFO] Task succeeded: fastANI
[2023-03-15 21:03:24,094] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 21:03:24,094] [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_002696205.1	s__UBA1479 sp002696205	93.3642	765	962	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	82.0955	735	962	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	81.8214	631	962	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_002433335.1	s__UBA1479 sp002433335	81.3121	601	962	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_002781745.1	s__UBA1479 sp002781745	81.3014	633	962	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_016765655.1	s__Skermanella mucosa	76.0898	150	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900230255.1	s__Caenispirillum bisanense	76.0747	154	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Caenispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590795.1	s__Azospirillum sp003590795	76.0332	122	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018699755.1	s__JABIRQ01 sp018699755	75.7668	88	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CADEGL01;f__CADEGL01;g__JABIRQ01	95.0	98.91	98.91	0.81	0.81	2	-
GCF_900177325.1	s__Mesorhizobium_A australicum_A	75.3284	86	962	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 21:03:24,094] [INFO] GTDB search result was written to OceanDNA-b30955/result_gtdb.tsv
[2023-03-15 21:03:24,094] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:03:24,096] [INFO] DFAST_QC result json was written to OceanDNA-b30955/dqc_result.json
[2023-03-15 21:03:24,096] [INFO] DFAST_QC completed!
[2023-03-15 21:03:24,096] [INFO] Total running time: 0h1m40s