[2023-03-17 02:03:49,437] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:03:49,437] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:03:49,437] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e6d4a29-6e86-4f51-8e3c-aa9465e4e6fb/dqc_reference
[2023-03-17 02:03:50,614] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:03:50,614] [INFO] Task started: Prodigal
[2023-03-17 02:03:50,614] [INFO] Running command: cat /var/lib/cwl/stg07b18de5-db72-4fb2-96a7-827ad840f71d/OceanDNA-b30970.fa | prodigal -d OceanDNA-b30970/cds.fna -a OceanDNA-b30970/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:04:07,913] [INFO] Task succeeded: Prodigal
[2023-03-17 02:04:07,913] [INFO] Task started: HMMsearch
[2023-03-17 02:04:07,913] [INFO] Running command: hmmsearch --tblout OceanDNA-b30970/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e6d4a29-6e86-4f51-8e3c-aa9465e4e6fb/dqc_reference/reference_markers.hmm OceanDNA-b30970/protein.faa > /dev/null
[2023-03-17 02:04:08,089] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:04:08,089] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg07b18de5-db72-4fb2-96a7-827ad840f71d/OceanDNA-b30970.fa]
[2023-03-17 02:04:08,109] [INFO] Query marker FASTA was written to OceanDNA-b30970/markers.fasta
[2023-03-17 02:04:08,110] [INFO] Task started: Blastn
[2023-03-17 02:04:08,110] [INFO] Running command: blastn -query OceanDNA-b30970/markers.fasta -db /var/lib/cwl/stg1e6d4a29-6e86-4f51-8e3c-aa9465e4e6fb/dqc_reference/reference_markers.fasta -out OceanDNA-b30970/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:04:08,689] [INFO] Task succeeded: Blastn
[2023-03-17 02:04:08,689] [INFO] Selected 18 target genomes.
[2023-03-17 02:04:08,690] [INFO] Target genome list was writen to OceanDNA-b30970/target_genomes.txt
[2023-03-17 02:04:08,700] [INFO] Task started: fastANI
[2023-03-17 02:04:08,700] [INFO] Running command: fastANI --query /var/lib/cwl/stg07b18de5-db72-4fb2-96a7-827ad840f71d/OceanDNA-b30970.fa --refList OceanDNA-b30970/target_genomes.txt --output OceanDNA-b30970/fastani_result.tsv --threads 1
[2023-03-17 02:04:23,797] [INFO] Task succeeded: fastANI
[2023-03-17 02:04:23,797] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e6d4a29-6e86-4f51-8e3c-aa9465e4e6fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:04:23,797] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e6d4a29-6e86-4f51-8e3c-aa9465e4e6fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:04:23,807] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:04:23,807] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 02:04:23,807] [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	76.7528	216	936	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	76.4995	152	936	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.4602	182	936	95	below_threshold
Minwuia thermotolerans	strain=SY3-15	GCA_002924445.1	2056226	2056226	type	True	76.448	168	936	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	76.4292	131	936	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.3795	170	936	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	76.3731	191	936	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.3727	221	936	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.351	220	936	95	below_threshold
Azospirillum soli	strain=CC-LY788	GCA_017876165.1	1304799	1304799	type	True	76.2593	195	936	95	below_threshold
Oceanibacterium hippocampi	strain=CECT 7691	GCA_900172325.1	745714	745714	type	True	76.0692	155	936	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	76.0457	130	936	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	75.8886	160	936	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	75.8452	171	936	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	75.7603	136	936	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	75.6573	130	936	95	below_threshold
Gemmobacter straminiformis	strain=CAM-8	GCA_014243445.1	2045119	2045119	type	True	75.6144	83	936	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 02:04:23,807] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30970/tc_result.tsv
[2023-03-17 02:04:23,807] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:04:23,808] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:04:23,808] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e6d4a29-6e86-4f51-8e3c-aa9465e4e6fb/dqc_reference/checkm_data
[2023-03-17 02:04:23,808] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:04:23,813] [INFO] Task started: CheckM
[2023-03-17 02:04:23,813] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30970/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30970/checkm_input OceanDNA-b30970/checkm_result
[2023-03-17 02:05:07,985] [INFO] Task succeeded: CheckM
[2023-03-17 02:05:07,985] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.80%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 02:05:07,988] [INFO] ===== Completeness check finished =====
[2023-03-17 02:05:07,988] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:05:07,988] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30970/markers.fasta)
[2023-03-17 02:05:07,988] [INFO] Task started: Blastn
[2023-03-17 02:05:07,988] [INFO] Running command: blastn -query OceanDNA-b30970/markers.fasta -db /var/lib/cwl/stg1e6d4a29-6e86-4f51-8e3c-aa9465e4e6fb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30970/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:05:08,871] [INFO] Task succeeded: Blastn
[2023-03-17 02:05:08,872] [INFO] Selected 8 target genomes.
[2023-03-17 02:05:08,872] [INFO] Target genome list was writen to OceanDNA-b30970/target_genomes_gtdb.txt
[2023-03-17 02:05:09,093] [INFO] Task started: fastANI
[2023-03-17 02:05:09,093] [INFO] Running command: fastANI --query /var/lib/cwl/stg07b18de5-db72-4fb2-96a7-827ad840f71d/OceanDNA-b30970.fa --refList OceanDNA-b30970/target_genomes_gtdb.txt --output OceanDNA-b30970/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:05:15,655] [INFO] Task succeeded: fastANI
[2023-03-17 02:05:15,661] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 02:05:15,661] [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	90.7545	867	936	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	87.7917	764	936	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	84.9351	681	936	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	82.7132	622	936	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	81.5154	606	936	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_002686255.1	s__Casp-alpha2 sp002686255	77.186	183	936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.76	99.74	0.90	0.88	3	-
GCF_016765655.1	s__Skermanella mucosa	76.3847	192	936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001511835.1	s__Phaeospirillum sp001511835	76.3216	181	936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 02:05:15,661] [INFO] GTDB search result was written to OceanDNA-b30970/result_gtdb.tsv
[2023-03-17 02:05:15,661] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:05:15,663] [INFO] DFAST_QC result json was written to OceanDNA-b30970/dqc_result.json
[2023-03-17 02:05:15,663] [INFO] DFAST_QC completed!
[2023-03-17 02:05:15,663] [INFO] Total running time: 0h1m26s