[2023-03-16 09:06:46,770] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:06:46,770] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:06:46,770] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ef2345b-81ef-43bb-a2fa-7883de90cbe5/dqc_reference
[2023-03-16 09:06:47,884] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:06:47,885] [INFO] Task started: Prodigal
[2023-03-16 09:06:47,885] [INFO] Running command: cat /var/lib/cwl/stg6b0646b0-11ac-4446-9416-92f4bccaf506/OceanDNA-b46916.fa | prodigal -d OceanDNA-b46916/cds.fna -a OceanDNA-b46916/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:07:38,900] [INFO] Task succeeded: Prodigal
[2023-03-16 09:07:38,901] [INFO] Task started: HMMsearch
[2023-03-16 09:07:38,901] [INFO] Running command: hmmsearch --tblout OceanDNA-b46916/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ef2345b-81ef-43bb-a2fa-7883de90cbe5/dqc_reference/reference_markers.hmm OceanDNA-b46916/protein.faa > /dev/null
[2023-03-16 09:07:39,166] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:07:39,167] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6b0646b0-11ac-4446-9416-92f4bccaf506/OceanDNA-b46916.fa]
[2023-03-16 09:07:39,212] [INFO] Query marker FASTA was written to OceanDNA-b46916/markers.fasta
[2023-03-16 09:07:39,213] [INFO] Task started: Blastn
[2023-03-16 09:07:39,213] [INFO] Running command: blastn -query OceanDNA-b46916/markers.fasta -db /var/lib/cwl/stg3ef2345b-81ef-43bb-a2fa-7883de90cbe5/dqc_reference/reference_markers.fasta -out OceanDNA-b46916/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:07:39,831] [INFO] Task succeeded: Blastn
[2023-03-16 09:07:39,835] [INFO] Selected 28 target genomes.
[2023-03-16 09:07:39,835] [INFO] Target genome list was writen to OceanDNA-b46916/target_genomes.txt
[2023-03-16 09:07:40,136] [INFO] Task started: fastANI
[2023-03-16 09:07:40,136] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b0646b0-11ac-4446-9416-92f4bccaf506/OceanDNA-b46916.fa --refList OceanDNA-b46916/target_genomes.txt --output OceanDNA-b46916/fastani_result.tsv --threads 1
[2023-03-16 09:08:03,690] [INFO] Task succeeded: fastANI
[2023-03-16 09:08:03,691] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ef2345b-81ef-43bb-a2fa-7883de90cbe5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:08:03,691] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ef2345b-81ef-43bb-a2fa-7883de90cbe5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:08:03,701] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:08:03,701] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 09:08:03,701] [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
Luteolibacter ambystomatis	strain=32A	GCA_018137965.1	2824561	2824561	type	True	76.0215	69	1962	95	below_threshold
Haloferula rosea	strain=KCTC 22201	GCA_016595525.1	490093	490093	type	True	75.7336	61	1962	95	below_threshold
Luteolibacter luteus	strain=G-1-1-1	GCA_012913485.1	2728835	2728835	type	True	75.5979	68	1962	95	below_threshold
Verrucomicrobium spinosum	strain=DSM 4136	GCA_000172155.1	2736	2736	type	True	75.4511	64	1962	95	below_threshold
Luteolibacter yonseiensis	strain=JCM 18052	GCA_016595465.1	1144680	1144680	type	True	75.4216	69	1962	95	below_threshold
Prosthecobacter vanneervenii	strain=DSM 12252	GCA_014203095.1	48466	48466	type	True	75.2987	72	1962	95	below_threshold
Roseimicrobium gellanilyticum	strain=DSM 25532	GCA_003315205.1	748857	748857	type	True	75.1218	58	1962	95	below_threshold
Arenimonas terrae	strain=R29	GCA_006265115.1	2546226	2546226	type	True	75.0507	55	1962	95	below_threshold
Chthoniobacter flavus	strain=Ellin428	GCA_000173075.1	191863	191863	type	True	74.976	71	1962	95	below_threshold
Chthoniobacter flavus	strain=DSM 22515	GCA_004341915.1	191863	191863	type	True	74.9745	71	1962	95	below_threshold
Arenimonas metalli	strain=CF5-1	GCA_000747155.1	948077	948077	type	True	74.8798	66	1962	95	below_threshold
Micromonospora gifhornensis	strain=NBRC 16317	GCA_016863515.1	84594	84594	type	True	74.7878	66	1962	95	below_threshold
Micromonospora terminaliae	strain=TMS7	GCA_010671825.1	1914461	1914461	type	True	74.6979	103	1962	95	below_threshold
Micromonospora pattaloongensis	strain=DSM 45245	GCA_900107255.1	405436	405436	type	True	74.6882	80	1962	95	below_threshold
Prauserella aidingensis	strain=DSM 45266	GCA_024171865.1	387890	387890	type	True	74.6119	60	1962	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 09:08:03,703] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46916/tc_result.tsv
[2023-03-16 09:08:03,706] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:08:03,706] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:08:03,706] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ef2345b-81ef-43bb-a2fa-7883de90cbe5/dqc_reference/checkm_data
[2023-03-16 09:08:03,707] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:08:04,026] [INFO] Task started: CheckM
[2023-03-16 09:08:04,026] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46916/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46916/checkm_input OceanDNA-b46916/checkm_result
[2023-03-16 09:10:07,392] [INFO] Task succeeded: CheckM
[2023-03-16 09:10:07,393] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.28%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 09:10:07,444] [INFO] ===== Completeness check finished =====
[2023-03-16 09:10:07,444] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:10:07,444] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46916/markers.fasta)
[2023-03-16 09:10:07,447] [INFO] Task started: Blastn
[2023-03-16 09:10:07,447] [INFO] Running command: blastn -query OceanDNA-b46916/markers.fasta -db /var/lib/cwl/stg3ef2345b-81ef-43bb-a2fa-7883de90cbe5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46916/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:10:09,036] [INFO] Task succeeded: Blastn
[2023-03-16 09:10:09,043] [INFO] Selected 24 target genomes.
[2023-03-16 09:10:09,043] [INFO] Target genome list was writen to OceanDNA-b46916/target_genomes_gtdb.txt
[2023-03-16 09:10:09,324] [INFO] Task started: fastANI
[2023-03-16 09:10:09,324] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b0646b0-11ac-4446-9416-92f4bccaf506/OceanDNA-b46916.fa --refList OceanDNA-b46916/target_genomes_gtdb.txt --output OceanDNA-b46916/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:10:26,668] [INFO] Task succeeded: fastANI
[2023-03-16 09:10:26,679] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 09:10:26,679] [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
GCF_014904755.1	s__Haloferula sp014904755	75.9432	136	1962	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795505.1	s__JAEUHH01 sp016795505	75.9333	121	1962	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__JAEUHH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002344525.1	s__Arctic95D-9 sp002344525	75.9213	118	1962	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007123695.1	s__Arctic95D-9 sp007123695	75.901	114	1962	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001695.1	s__Roseibacillus_B sp013001695	75.8646	140	1962	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Roseibacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007123195.1	s__SKLO01 sp007123195	75.8437	103	1962	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__SKLO01;g__SKLO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017798145.1	s__Luteolibacter sp017798145	75.7784	75	1962	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Luteolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002304315.1	s__Haloferula sp002304315	75.6865	80	1962	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019186985.1	s__Prosthecobacter sp019186985	75.6243	91	1962	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012913485.1	s__Haloferula lutea	75.5778	67	1962	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795385.1	s__Arctic95D-9 sp016795385	75.5016	109	1962	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795375.1	s__Prosthecobacter sp016795375	75.4496	72	1962	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Prosthecobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011044495.1	s__Roseimicrobium sp011044495	75.3188	51	1962	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Verrucomicrobiaceae;g__Roseimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009885995.1	s__VFJQ01 sp009885995	75.3063	94	1962	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Chthoniobacterales;f__Chthoniobacteraceae;g__VFJQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000739615.1	s__Haloferula sp000739615	75.2397	102	1962	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871615.1	s__SXXZ01 sp016871615	75.1059	82	1962	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__SXXZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871675.1	s__VHCN01 sp016871675	74.9423	57	1962	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__VHCN01;g__VHCN01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001580455.1	s__Ramlibacter tataouinensis_B	74.7878	54	1962	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 09:10:26,682] [INFO] GTDB search result was written to OceanDNA-b46916/result_gtdb.tsv
[2023-03-16 09:10:26,686] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:10:26,692] [INFO] DFAST_QC result json was written to OceanDNA-b46916/dqc_result.json
[2023-03-16 09:10:26,692] [INFO] DFAST_QC completed!
[2023-03-16 09:10:26,692] [INFO] Total running time: 0h3m40s