[2023-03-16 09:13:21,024] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:13:21,025] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:13:21,025] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b07ce97-b4dc-47bb-b195-54dcd8964a54/dqc_reference
[2023-03-16 09:13:22,472] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:13:22,472] [INFO] Task started: Prodigal
[2023-03-16 09:13:22,473] [INFO] Running command: cat /var/lib/cwl/stg07f6e795-57af-496b-bfa3-6c59a3838a73/OceanDNA-b22114.fa | prodigal -d OceanDNA-b22114/cds.fna -a OceanDNA-b22114/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:13:41,701] [INFO] Task succeeded: Prodigal
[2023-03-16 09:13:41,701] [INFO] Task started: HMMsearch
[2023-03-16 09:13:41,701] [INFO] Running command: hmmsearch --tblout OceanDNA-b22114/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b07ce97-b4dc-47bb-b195-54dcd8964a54/dqc_reference/reference_markers.hmm OceanDNA-b22114/protein.faa > /dev/null
[2023-03-16 09:13:41,911] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:13:41,912] [INFO] Found 6/6 markers.
[2023-03-16 09:13:41,951] [INFO] Query marker FASTA was written to OceanDNA-b22114/markers.fasta
[2023-03-16 09:13:41,952] [INFO] Task started: Blastn
[2023-03-16 09:13:41,953] [INFO] Running command: blastn -query OceanDNA-b22114/markers.fasta -db /var/lib/cwl/stg0b07ce97-b4dc-47bb-b195-54dcd8964a54/dqc_reference/reference_markers.fasta -out OceanDNA-b22114/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:13:42,555] [INFO] Task succeeded: Blastn
[2023-03-16 09:13:42,570] [INFO] Selected 28 target genomes.
[2023-03-16 09:13:42,571] [INFO] Target genome list was writen to OceanDNA-b22114/target_genomes.txt
[2023-03-16 09:13:42,583] [INFO] Task started: fastANI
[2023-03-16 09:13:42,583] [INFO] Running command: fastANI --query /var/lib/cwl/stg07f6e795-57af-496b-bfa3-6c59a3838a73/OceanDNA-b22114.fa --refList OceanDNA-b22114/target_genomes.txt --output OceanDNA-b22114/fastani_result.tsv --threads 1
[2023-03-16 09:14:03,679] [INFO] Task succeeded: fastANI
[2023-03-16 09:14:03,679] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b07ce97-b4dc-47bb-b195-54dcd8964a54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:14:03,679] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b07ce97-b4dc-47bb-b195-54dcd8964a54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:14:03,690] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:14:03,690] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 09:14:03,690] [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
Algisphaera agarilytica	strain=DSM 103725	GCA_014207595.1	1385975	1385975	type	True	76.4357	97	1041	95	below_threshold
Mucisphaera calidilacus	strain=Pan265	GCA_007748075.1	2527982	2527982	type	True	75.9791	80	1041	95	below_threshold
Phycisphaera mikurensis	strain=DSM 103959	GCA_014207395.1	547188	547188	type	True	75.95	107	1041	95	below_threshold
Phycisphaera mikurensis	strain=NBRC 102666	GCA_000284115.1	547188	547188	type	True	75.9337	110	1041	95	below_threshold
Humisphaera borealis	strain=M1803	GCA_015169395.1	2807512	2807512	type	True	75.4538	69	1041	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	75.3091	92	1041	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	75.2302	92	1041	95	below_threshold
Nocardioides kribbensis	strain=DSM 16314	GCA_015070375.1	305517	305517	type	True	75.0728	66	1041	95	below_threshold
Nocardioides dokdonensis	strain=FR1436	GCA_001653335.1	450734	450734	type	True	74.9703	51	1041	95	below_threshold
Geodermatophilus chilensis	strain=B12	GCA_002802985.1	2035835	2035835	type	True	74.9465	60	1041	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_003387045.1	34007	34007	type	True	74.8234	54	1041	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_000763885.1	34007	34007	type	True	74.8144	54	1041	95	below_threshold
Micromonospora coxensis	strain=DSM 45161	GCA_900090295.1	356852	356852	type	True	74.6915	98	1041	95	below_threshold
Actinomadura formosensis	strain=NBRC 14204	GCA_001552155.1	60706	60706	type	True	74.6549	59	1041	95	below_threshold
Geodermatophilus obscurus	strain=DSM 43160	GCA_000025345.1	1861	1861	type	True	74.6345	68	1041	95	below_threshold
Nocardioides litoris	strain=DSM 103718	GCA_006346315.1	1926648	1926648	type	True	74.6311	73	1041	95	below_threshold
Actinomadura madurae	strain=DSM 43067	GCA_900115095.1	1993	1993	type	True	74.6141	104	1041	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 09:14:03,697] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22114/tc_result.tsv
[2023-03-16 09:14:03,706] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:14:03,707] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:14:03,707] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b07ce97-b4dc-47bb-b195-54dcd8964a54/dqc_reference/checkm_data
[2023-03-16 09:14:03,708] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:14:03,714] [INFO] Task started: CheckM
[2023-03-16 09:14:03,714] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22114/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22114/checkm_input OceanDNA-b22114/checkm_result
[2023-03-16 09:14:54,231] [INFO] Task succeeded: CheckM
[2023-03-16 09:14:54,231] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 09:14:54,333] [INFO] ===== Completeness check finished =====
[2023-03-16 09:14:54,334] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:14:54,334] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22114/markers.fasta)
[2023-03-16 09:14:54,335] [INFO] Task started: Blastn
[2023-03-16 09:14:54,335] [INFO] Running command: blastn -query OceanDNA-b22114/markers.fasta -db /var/lib/cwl/stg0b07ce97-b4dc-47bb-b195-54dcd8964a54/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22114/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:14:55,342] [INFO] Task succeeded: Blastn
[2023-03-16 09:14:55,372] [INFO] Selected 24 target genomes.
[2023-03-16 09:14:55,372] [INFO] Target genome list was writen to OceanDNA-b22114/target_genomes_gtdb.txt
[2023-03-16 09:14:55,443] [INFO] Task started: fastANI
[2023-03-16 09:14:55,443] [INFO] Running command: fastANI --query /var/lib/cwl/stg07f6e795-57af-496b-bfa3-6c59a3838a73/OceanDNA-b22114.fa --refList OceanDNA-b22114/target_genomes_gtdb.txt --output OceanDNA-b22114/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:15:08,697] [INFO] Task succeeded: fastANI
[2023-03-16 09:15:08,709] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 09:15:08,710] [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_003696675.1	s__UBA6054 sp003696675	77.0737	120	1041	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA6054	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017303565.1	s__JAFLCM01 sp017303565	77.0237	128	1041	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JAFLCM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002337215.1	s__UBA1926 sp002337215	77.007	140	1041	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1926	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013285505.1	s__PNC22 sp013285505	76.9216	161	1041	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__PNC22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693765.1	s__RECZ01 sp007693765	76.9119	168	1041	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__RECZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002429045.1	s__UBA6054 sp002429045	76.8866	143	1041	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA6054	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007694925.1	s__SLFH01 sp007694925	76.8599	145	1041	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__SLFH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693965.1	s__RECQ01 sp007693965	76.7927	157	1041	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__RECQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016742075.1	s__JACVCL01 sp016742075	76.7917	165	1041	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JACVCL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693725.1	s__REDD01 sp007693725	76.7768	152	1041	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__REDD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003511945.1	s__UBA11155 sp003511945	76.6717	124	1041	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA11155	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693785.1	s__RECY01 sp007693785	76.6421	150	1041	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__RECY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903929885.1	s__UBA2402 sp903929885	76.5922	101	1041	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA2402	95.0	99.77	99.77	0.95	0.95	2	-
GCA_013360695.1	s__JABWBC01 sp013360695	76.5354	111	1041	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JABWBC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011331335.1	s__DSSA01 sp011331335	76.514	125	1041	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__DSSA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709445.1	s__PNC22 sp016709445	76.4739	136	1041	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__PNC22	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364005.1	s__UBA1924 sp002364005	76.4448	111	1041	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA1924	95.0	99.92	99.89	0.95	0.91	4	-
GCA_011053195.1	s__GCA-2732755 sp011053195	76.4361	73	1041	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__GCA-2732755	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016742055.1	s__JACVCK01 sp016742055	76.2481	123	1041	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JACVCK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793195.1	s__JABWBC01 sp016793195	76.191	118	1041	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__JABWBC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002343325.1	s__UBA2396 sp002343325	76.1661	92	1041	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__UBA2396	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 09:15:08,724] [INFO] GTDB search result was written to OceanDNA-b22114/result_gtdb.tsv
[2023-03-16 09:15:08,741] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:15:08,759] [INFO] DFAST_QC result json was written to OceanDNA-b22114/dqc_result.json
[2023-03-16 09:15:08,759] [INFO] DFAST_QC completed!
[2023-03-16 09:15:08,759] [INFO] Total running time: 0h1m48s