[2023-03-17 00:17:04,657] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:17:04,657] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:17:04,657] [INFO] DQC Reference Directory: /var/lib/cwl/stg9e446522-fc10-4b9c-8b7e-5f78f4ecdf35/dqc_reference
[2023-03-17 00:17:05,770] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:17:05,770] [INFO] Task started: Prodigal
[2023-03-17 00:17:05,770] [INFO] Running command: cat /var/lib/cwl/stgce33c8be-5169-45fd-8298-f833c9171eeb/OceanDNA-b23019.fa | prodigal -d OceanDNA-b23019/cds.fna -a OceanDNA-b23019/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:17:36,230] [INFO] Task succeeded: Prodigal
[2023-03-17 00:17:36,231] [INFO] Task started: HMMsearch
[2023-03-17 00:17:36,231] [INFO] Running command: hmmsearch --tblout OceanDNA-b23019/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9e446522-fc10-4b9c-8b7e-5f78f4ecdf35/dqc_reference/reference_markers.hmm OceanDNA-b23019/protein.faa > /dev/null
[2023-03-17 00:17:36,455] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:17:36,455] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgce33c8be-5169-45fd-8298-f833c9171eeb/OceanDNA-b23019.fa]
[2023-03-17 00:17:36,481] [INFO] Query marker FASTA was written to OceanDNA-b23019/markers.fasta
[2023-03-17 00:17:36,482] [INFO] Task started: Blastn
[2023-03-17 00:17:36,482] [INFO] Running command: blastn -query OceanDNA-b23019/markers.fasta -db /var/lib/cwl/stg9e446522-fc10-4b9c-8b7e-5f78f4ecdf35/dqc_reference/reference_markers.fasta -out OceanDNA-b23019/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:17:37,063] [INFO] Task succeeded: Blastn
[2023-03-17 00:17:37,063] [INFO] Selected 25 target genomes.
[2023-03-17 00:17:37,064] [INFO] Target genome list was writen to OceanDNA-b23019/target_genomes.txt
[2023-03-17 00:17:37,079] [INFO] Task started: fastANI
[2023-03-17 00:17:37,079] [INFO] Running command: fastANI --query /var/lib/cwl/stgce33c8be-5169-45fd-8298-f833c9171eeb/OceanDNA-b23019.fa --refList OceanDNA-b23019/target_genomes.txt --output OceanDNA-b23019/fastani_result.tsv --threads 1
[2023-03-17 00:17:56,173] [INFO] Task succeeded: fastANI
[2023-03-17 00:17:56,173] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9e446522-fc10-4b9c-8b7e-5f78f4ecdf35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:17:56,174] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9e446522-fc10-4b9c-8b7e-5f78f4ecdf35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:17:56,185] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:17:56,185] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 00:17:56,185] [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
Pseudoxanthomonas taiwanensis	strain=DSM 22914	GCA_010093135.1	176598	176598	type	True	75.3053	53	1233	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	75.1832	63	1233	95	below_threshold
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	75.1082	64	1233	95	below_threshold
Asanoa ishikariensis	strain=NBRC 14551	GCA_016862535.1	137265	137265	type	True	74.9609	91	1233	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	74.96	98	1233	95	below_threshold
Asanoa ishikariensis	strain=DSM 44718	GCA_900107455.1	137265	137265	type	True	74.9456	94	1233	95	below_threshold
Blastococcus saxobsidens	strain=DSM 44509	GCA_002938435.1	138336	138336	type	True	74.9228	87	1233	95	below_threshold
Blastococcus saxobsidens	strain=DSM 44509	GCA_004217455.1	138336	138336	type	True	74.9225	87	1233	95	below_threshold
Asanoa siamensis	strain=NBRC 107932	GCA_016862555.1	926357	926357	type	True	74.9	99	1233	95	below_threshold
Pirellulimonas nuda	strain=Pla175	GCA_007750855.1	2528009	2528009	type	True	74.899	52	1233	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	74.8961	59	1233	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	74.8263	111	1233	95	below_threshold
Asanoa iriomotensis	strain=NBRC 100142	GCA_016862515.1	234613	234613	type	True	74.8125	116	1233	95	below_threshold
Sphaerisporangium melleum	strain=JCM 13064	GCA_014646695.1	321316	321316	type	True	74.7985	102	1233	95	below_threshold
Geodermatophilus poikilotrophus	strain=DSM 44209	GCA_900111455.1	1333667	1333667	type	True	74.7772	89	1233	95	below_threshold
Cereibacter sphaeroides	strain=NBRC 12203	GCA_007991035.1	1063	1063	type	True	74.7697	50	1233	95	below_threshold
Geodermatophilus saharensis	strain=DSM 45423	GCA_900188205.1	1137994	1137994	type	True	74.6895	104	1233	95	below_threshold
Paludisphaera rhizosphaereae	strain=JC665	GCA_011065895.1	2711216	2711216	type	True	74.6886	66	1233	95	below_threshold
[Luteovulum] sphaeroides subsp. megalophilum	strain=DSM 18937	GCA_900188265.1	418630	1063	type	True	74.6462	50	1233	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 00:17:56,185] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23019/tc_result.tsv
[2023-03-17 00:17:56,185] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:17:56,185] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:17:56,186] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9e446522-fc10-4b9c-8b7e-5f78f4ecdf35/dqc_reference/checkm_data
[2023-03-17 00:17:56,186] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:17:56,213] [INFO] Task started: CheckM
[2023-03-17 00:17:56,213] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23019/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23019/checkm_input OceanDNA-b23019/checkm_result
[2023-03-17 00:19:11,717] [INFO] Task succeeded: CheckM
[2023-03-17 00:19:11,717] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 00:19:11,744] [INFO] ===== Completeness check finished =====
[2023-03-17 00:19:11,745] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:19:11,745] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23019/markers.fasta)
[2023-03-17 00:19:11,746] [INFO] Task started: Blastn
[2023-03-17 00:19:11,746] [INFO] Running command: blastn -query OceanDNA-b23019/markers.fasta -db /var/lib/cwl/stg9e446522-fc10-4b9c-8b7e-5f78f4ecdf35/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23019/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:19:12,584] [INFO] Task succeeded: Blastn
[2023-03-17 00:19:12,589] [INFO] Selected 23 target genomes.
[2023-03-17 00:19:12,589] [INFO] Target genome list was writen to OceanDNA-b23019/target_genomes_gtdb.txt
[2023-03-17 00:19:12,703] [INFO] Task started: fastANI
[2023-03-17 00:19:12,704] [INFO] Running command: fastANI --query /var/lib/cwl/stgce33c8be-5169-45fd-8298-f833c9171eeb/OceanDNA-b23019.fa --refList OceanDNA-b23019/target_genomes_gtdb.txt --output OceanDNA-b23019/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:19:30,262] [INFO] Task succeeded: fastANI
[2023-03-17 00:19:30,274] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 00:19:30,275] [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_007751255.1	s__Pla86 sp007751255	78.538	475	1233	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__Pla86	95.0	100.00	100.00	1.00	1.00	2	-
GCA_007750655.1	s__Pla163 sp007750655	77.1358	301	1233	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__Pla163	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125265.1	s__RI-242 sp016125265	76.9248	200	1233	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__RI-242	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011053145.1	s__DRLC01 sp011053145	76.6167	134	1233	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__DRLC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826945.1	s__RBC036 sp902826945	76.5658	250	1233	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__RBC036	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009691855.1	s__JABFRZ01 sp009691855	76.5008	184	1233	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JABFRZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013360535.1	s__F1-120-MAGs118 sp013360535	76.498	159	1233	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__F1-120-MAGs118	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686265.1	s__GCA-2686265 sp002686265	76.4966	156	1233	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2686265	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712565.1	s__JADJQU01 sp016712565	76.4186	146	1233	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JADJQU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862085.1	s__GCA-2862085 sp002862085	76.3774	194	1233	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2862085	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872715.1	s__F1-120-MAGs118 sp016872715	76.3618	171	1233	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__F1-120-MAGs118	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013140785.1	s__JABFRZ01 sp013140785	76.2947	146	1233	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JABFRZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004296785.1	s__GW928-bin9 sp004296785	76.281	160	1233	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GW928-bin9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480285.1	s__GCA-2862085 sp905480285	76.2714	138	1233	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2862085	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872755.1	s__GW928-bin9 sp016872755	76.2206	181	1233	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GW928-bin9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903928115.1	s__F1-120-MAGs118 sp903928115	76.1103	189	1233	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__F1-120-MAGs118	95.0	99.83	99.80	0.95	0.95	3	-
GCA_011525785.1	s__WYBT01 sp011525785	75.9802	236	1233	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__WYBT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014237855.1	s__JABACD01 sp014237855	75.818	79	1233	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JABACD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004357655.1	s__N075bin59 sp004357655	75.815	152	1233	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__N075bin59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795245.1	s__JAEUIA01 sp016795245	75.7825	117	1233	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JAEUIA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007750855.1	s__Pirellulimonas nuda	74.8913	53	1233	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Pirellulimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646695.1	s__Sphaerisporangium melleum	74.7972	103	1233	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Sphaerisporangium	95.0	99.98	99.98	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2023-03-17 00:19:30,290] [INFO] GTDB search result was written to OceanDNA-b23019/result_gtdb.tsv
[2023-03-17 00:19:30,290] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:19:30,293] [INFO] DFAST_QC result json was written to OceanDNA-b23019/dqc_result.json
[2023-03-17 00:19:30,293] [INFO] DFAST_QC completed!
[2023-03-17 00:19:30,293] [INFO] Total running time: 0h2m26s