[2023-03-14 14:50:58,471] [INFO] DFAST_QC pipeline started.
[2023-03-14 14:50:58,471] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 14:50:58,471] [INFO] DQC Reference Directory: /var/lib/cwl/stg9fe5347c-b99b-4927-8af6-0bf5b8897815/dqc_reference
[2023-03-14 14:51:00,674] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 14:51:00,676] [INFO] Task started: Prodigal
[2023-03-14 14:51:00,677] [INFO] Running command: cat /var/lib/cwl/stg0c289ca7-fda8-457d-be01-40718620779b/OceanDNA-b20949.fa | prodigal -d OceanDNA-b20949/cds.fna -a OceanDNA-b20949/protein.faa -g 11 -q > /dev/null
[2023-03-14 14:51:22,973] [INFO] Task succeeded: Prodigal
[2023-03-14 14:51:22,973] [INFO] Task started: HMMsearch
[2023-03-14 14:51:22,973] [INFO] Running command: hmmsearch --tblout OceanDNA-b20949/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9fe5347c-b99b-4927-8af6-0bf5b8897815/dqc_reference/reference_markers.hmm OceanDNA-b20949/protein.faa > /dev/null
[2023-03-14 14:51:23,212] [INFO] Task succeeded: HMMsearch
[2023-03-14 14:51:23,213] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg0c289ca7-fda8-457d-be01-40718620779b/OceanDNA-b20949.fa]
[2023-03-14 14:51:23,251] [INFO] Query marker FASTA was written to OceanDNA-b20949/markers.fasta
[2023-03-14 14:51:23,252] [INFO] Task started: Blastn
[2023-03-14 14:51:23,252] [INFO] Running command: blastn -query OceanDNA-b20949/markers.fasta -db /var/lib/cwl/stg9fe5347c-b99b-4927-8af6-0bf5b8897815/dqc_reference/reference_markers.fasta -out OceanDNA-b20949/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:51:23,935] [INFO] Task succeeded: Blastn
[2023-03-14 14:51:23,936] [INFO] Selected 30 target genomes.
[2023-03-14 14:51:23,937] [INFO] Target genome list was writen to OceanDNA-b20949/target_genomes.txt
[2023-03-14 14:51:23,999] [INFO] Task started: fastANI
[2023-03-14 14:51:23,999] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c289ca7-fda8-457d-be01-40718620779b/OceanDNA-b20949.fa --refList OceanDNA-b20949/target_genomes.txt --output OceanDNA-b20949/fastani_result.tsv --threads 1
[2023-03-14 14:51:55,584] [INFO] Task succeeded: fastANI
[2023-03-14 14:51:55,584] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9fe5347c-b99b-4927-8af6-0bf5b8897815/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 14:51:55,585] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9fe5347c-b99b-4927-8af6-0bf5b8897815/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 14:51:55,605] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 14:51:55,605] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 14:51:55,605] [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
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	75.1698	76	913	95	below_threshold
Pseudoxanthomonas jiangsuensis	strain=DSM 22398	GCA_010093185.1	619688	619688	type	True	75.0883	91	913	95	below_threshold
Arenimonas metalli	strain=CF5-1	GCA_000747155.1	948077	948077	type	True	74.9721	72	913	95	below_threshold
Actinoplanes atraurantiacus	strain=CGMCC 4.6857	GCA_900215205.1	1036182	1036182	type	True	74.7826	148	913	95	below_threshold
Nonomuraea endophytica	strain=DSM 45385	GCA_014203235.1	714136	714136	type	True	74.779	144	913	95	below_threshold
Catellatospora sichuanensis	strain=H14505	GCA_007483665.1	1969805	1969805	type	True	74.7784	145	913	95	below_threshold
Salsipaludibacter albus	strain=AS10	GCA_019798055.1	2849650	2849650	type	True	74.7657	69	913	95	below_threshold
Rhizocola hellebori	strain=NBRC 109834	GCA_016862955.1	1392758	1392758	type	True	74.7594	65	913	95	below_threshold
Acidovorax cattleyae	strain=DSM 17101	GCA_900104515.1	80868	80868	type	True	74.7584	75	913	95	below_threshold
Nocardiopsis chromatogenes	strain=YIM 90109	GCA_000341185.1	280239	280239	type	True	74.7281	108	913	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	74.7221	83	913	95	below_threshold
Nonomuraea coxensis	strain=DSM 45129	GCA_000379885.1	404386	404386	type	True	74.6887	128	913	95	below_threshold
Nonomuraea coxensis	strain=DSM 45129	GCA_019397265.1	404386	404386	type	True	74.687	129	913	95	below_threshold
Glycomyces arizonensis	strain=DSM 44726	GCA_000482705.1	256035	256035	type	True	74.6685	69	913	95	below_threshold
Methylobacterium oxalidis	strain=DSM 24028	GCA_022179505.1	944322	944322	type	True	74.6538	80	913	95	below_threshold
Agromyces tardus	strain=SJ-23	GCA_003710805.1	2583849	2583849	type	True	74.6456	69	913	95	below_threshold
Agromyces kandeliae	strain=Q22	GCA_009674665.1	2666141	2666141	type	True	74.6444	61	913	95	below_threshold
Nonomuraea zeae	strain=DSM 100528	GCA_005889725.1	1642303	1642303	type	True	74.6339	141	913	95	below_threshold
Methylobacterium oxalidis	strain=NBRC 107715	GCA_007992195.1	944322	944322	type	True	74.5847	79	913	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 14:51:55,605] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20949/tc_result.tsv
[2023-03-14 14:51:55,605] [INFO] ===== Taxonomy check completed =====
[2023-03-14 14:51:55,605] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 14:51:55,605] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9fe5347c-b99b-4927-8af6-0bf5b8897815/dqc_reference/checkm_data
[2023-03-14 14:51:55,606] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 14:51:55,614] [INFO] Task started: CheckM
[2023-03-14 14:51:55,614] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20949/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20949/checkm_input OceanDNA-b20949/checkm_result
[2023-03-14 14:52:58,566] [INFO] Task succeeded: CheckM
[2023-03-14 14:52:58,567] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.99%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 14:52:58,570] [INFO] ===== Completeness check finished =====
[2023-03-14 14:52:58,570] [INFO] ===== Start GTDB Search =====
[2023-03-14 14:52:58,570] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20949/markers.fasta)
[2023-03-14 14:52:58,572] [INFO] Task started: Blastn
[2023-03-14 14:52:58,572] [INFO] Running command: blastn -query OceanDNA-b20949/markers.fasta -db /var/lib/cwl/stg9fe5347c-b99b-4927-8af6-0bf5b8897815/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20949/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:53:00,768] [INFO] Task succeeded: Blastn
[2023-03-14 14:53:00,770] [INFO] Selected 24 target genomes.
[2023-03-14 14:53:00,770] [INFO] Target genome list was writen to OceanDNA-b20949/target_genomes_gtdb.txt
[2023-03-14 14:53:00,818] [INFO] Task started: fastANI
[2023-03-14 14:53:00,818] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c289ca7-fda8-457d-be01-40718620779b/OceanDNA-b20949.fa --refList OceanDNA-b20949/target_genomes_gtdb.txt --output OceanDNA-b20949/fastani_result_gtdb.tsv --threads 1
[2023-03-14 14:53:30,277] [INFO] Task succeeded: fastANI
[2023-03-14 14:53:30,288] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 14:53:30,288] [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_002343455.1	s__UBA2385 sp002343455	76.1662	234	913	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__UBA2385	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016717595.1	s__JADKFE01 sp016717595	76.0498	186	913	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__CAJQPC01;g__JADKFE01	95.0	98.32	98.16	0.91	0.88	3	-
GCA_006226595.1	s__M1803 sp006226595	75.8866	154	913	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__GCA-2862545;g__M1803	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903921785.1	s__SXON01 sp903921785	75.7785	155	913	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__SXON01	95.0	99.91	99.91	0.96	0.95	4	-
GCA_016875435.1	s__SXON01 sp016875435	75.7589	136	913	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__SXON01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903875225.1	s__CAIUMM01 sp903875225	75.6616	123	913	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__CAIUMM01	95.0	99.62	99.43	0.93	0.90	4	-
GCA_013152105.1	s__UBA2385 sp013152105	75.651	111	913	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__UBA2385	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903844155.1	s__CAIUMM01 sp903844155	75.4057	102	913	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__CAIUMM01	95.0	99.98	99.97	0.97	0.97	4	-
GCA_016792625.1	s__JAEUKK01 sp016792625	75.3947	212	913	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__JAEUKK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014191855.1	s__SXON01 sp014191855	75.2735	100	913	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__SXON01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009469595.1	s__Thauera sp009469595	74.9459	53	913	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Thauera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012798435.1	s__JAAZNF01 sp012798435	74.8739	75	913	d__Bacteria;p__Myxococcota;c__B64-G9;o__B64-G9;f__B64-G9;g__JAAZNF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009692555.1	s__SHYY01 sp009692555	74.804	72	913	d__Bacteria;p__Myxococcota;c__Polyangia;o__Palsa-1104;f__Palsa-1104;g__SHYY01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007483665.1	s__Catellatospora sichuanensis	74.7785	147	913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009806555.1	s__Methylobacterium sp009806555	74.7703	60	913	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428945.1	s__Hamadaea tsunoensis	74.7051	112	913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Hamadaea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713225.1	s__JADJPO01 sp016713225	74.6375	61	913	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__JADJPO01	95.0	99.38	99.28	0.94	0.94	3	-
GCF_007992195.1	s__Methylobacterium oxalidis	74.6154	81	913	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 14:53:30,288] [INFO] GTDB search result was written to OceanDNA-b20949/result_gtdb.tsv
[2023-03-14 14:53:30,288] [INFO] ===== GTDB Search completed =====
[2023-03-14 14:53:30,290] [INFO] DFAST_QC result json was written to OceanDNA-b20949/dqc_result.json
[2023-03-14 14:53:30,291] [INFO] DFAST_QC completed!
[2023-03-14 14:53:30,291] [INFO] Total running time: 0h2m32s