[2023-03-16 00:33:46,277] [INFO] DFAST_QC pipeline started.
[2023-03-16 00:33:46,302] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 00:33:46,303] [INFO] DQC Reference Directory: /var/lib/cwl/stg97d82199-989b-4851-bbfd-c1ff28f52039/dqc_reference
[2023-03-16 00:33:47,456] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 00:33:47,456] [INFO] Task started: Prodigal
[2023-03-16 00:33:47,456] [INFO] Running command: cat /var/lib/cwl/stg85370f69-6d24-4cb4-8dd0-49cd6dfdf487/OceanDNA-b2515.fa | prodigal -d OceanDNA-b2515/cds.fna -a OceanDNA-b2515/protein.faa -g 11 -q > /dev/null
[2023-03-16 00:33:56,927] [INFO] Task succeeded: Prodigal
[2023-03-16 00:33:56,927] [INFO] Task started: HMMsearch
[2023-03-16 00:33:56,927] [INFO] Running command: hmmsearch --tblout OceanDNA-b2515/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg97d82199-989b-4851-bbfd-c1ff28f52039/dqc_reference/reference_markers.hmm OceanDNA-b2515/protein.faa > /dev/null
[2023-03-16 00:33:57,076] [INFO] Task succeeded: HMMsearch
[2023-03-16 00:33:57,077] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg85370f69-6d24-4cb4-8dd0-49cd6dfdf487/OceanDNA-b2515.fa]
[2023-03-16 00:33:57,091] [INFO] Query marker FASTA was written to OceanDNA-b2515/markers.fasta
[2023-03-16 00:33:57,092] [INFO] Task started: Blastn
[2023-03-16 00:33:57,092] [INFO] Running command: blastn -query OceanDNA-b2515/markers.fasta -db /var/lib/cwl/stg97d82199-989b-4851-bbfd-c1ff28f52039/dqc_reference/reference_markers.fasta -out OceanDNA-b2515/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:33:57,779] [INFO] Task succeeded: Blastn
[2023-03-16 00:33:57,779] [INFO] Selected 19 target genomes.
[2023-03-16 00:33:57,780] [INFO] Target genome list was writen to OceanDNA-b2515/target_genomes.txt
[2023-03-16 00:33:57,864] [INFO] Task started: fastANI
[2023-03-16 00:33:57,864] [INFO] Running command: fastANI --query /var/lib/cwl/stg85370f69-6d24-4cb4-8dd0-49cd6dfdf487/OceanDNA-b2515.fa --refList OceanDNA-b2515/target_genomes.txt --output OceanDNA-b2515/fastani_result.tsv --threads 1
[2023-03-16 00:34:15,782] [INFO] Task succeeded: fastANI
[2023-03-16 00:34:15,782] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg97d82199-989b-4851-bbfd-c1ff28f52039/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 00:34:15,783] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg97d82199-989b-4851-bbfd-c1ff28f52039/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 00:34:15,794] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 00:34:15,794] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 00:34:15,794] [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
Carbonactinospora thermoautotrophica	strain=UBT1	GCA_001543915.1	1469144	1469144	type	True	76.5149	66	250	95	below_threshold
Motilibacter aurantiacus	strain=K478	GCA_011250645.1	2714955	2714955	type	True	76.2169	120	250	95	below_threshold
Motilibacter rhizosphaerae	strain=DSM 45622	GCA_004216915.1	598652	598652	type	True	76.1028	122	250	95	below_threshold
Carbonactinospora thermoautotrophica	strain=UBT1	GCA_001543895.1	1469144	1469144	type	True	76.097	89	250	95	below_threshold
Nocardioides perillae	strain=DSM 24552	GCA_013409425.1	1119534	1119534	type	True	76.0647	125	250	95	below_threshold
Motilibacter deserti	strain=E257	GCA_011250635.1	2714956	2714956	type	True	76.0189	110	250	95	below_threshold
Planotetraspora thailandica	strain=NBRC 104271	GCA_016863335.1	487172	487172	type	True	75.862	85	250	95	below_threshold
Frankia saprophytica	strain=CN3	GCA_000235425.3	298655	298655	type	True	75.8335	123	250	95	below_threshold
Pseudokineococcus marinus	strain=JCM 14547	GCA_013004605.1	351215	351215	type	True	75.8207	117	250	95	below_threshold
Pseudonocardia hierapolitana	strain=DSM 45671	GCA_007994075.1	1128676	1128676	type	True	75.7714	130	250	95	below_threshold
Jiangella alba	strain=YIM 61503	GCA_001708125.1	561176	561176	type	True	75.684	134	250	95	below_threshold
Jiangella alba	strain=DSM 45237	GCA_900106035.1	561176	561176	type	True	75.6824	134	250	95	below_threshold
Pseudonocardia kunmingensis	strain=DSM 45301	GCA_006716445.1	630975	630975	type	True	75.6741	140	250	95	below_threshold
Actinomadura geliboluensis	strain=A8036	GCA_005889745.1	882440	882440	type	True	75.6582	133	250	95	below_threshold
Jiangella rhizosphaerae	strain=NEAU-YY265	GCA_003579925.1	2293569	2293569	type	True	75.5638	128	250	95	below_threshold
Jiangella muralis	strain=DSM 45357	GCA_001270745.1	702383	702383	type	True	75.5219	134	250	95	below_threshold
Jiangella gansuensis	strain=DSM 44835	GCA_000515395.1	281473	281473	type	True	75.4786	96	250	95	below_threshold
Prauserella muralis	strain=DSM 45305	GCA_003202285.1	588067	588067	type	True	75.3998	110	250	95	below_threshold
Prauserella muralis	strain=DSM 45305	GCA_007993965.1	588067	588067	type	True	75.3815	112	250	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 00:34:15,794] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2515/tc_result.tsv
[2023-03-16 00:34:15,794] [INFO] ===== Taxonomy check completed =====
[2023-03-16 00:34:15,794] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 00:34:15,795] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg97d82199-989b-4851-bbfd-c1ff28f52039/dqc_reference/checkm_data
[2023-03-16 00:34:15,795] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 00:34:15,840] [INFO] Task started: CheckM
[2023-03-16 00:34:15,840] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2515/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2515/checkm_input OceanDNA-b2515/checkm_result
[2023-03-16 00:34:43,610] [INFO] Task succeeded: CheckM
[2023-03-16 00:34:43,610] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.80%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 00:34:43,659] [INFO] ===== Completeness check finished =====
[2023-03-16 00:34:43,659] [INFO] ===== Start GTDB Search =====
[2023-03-16 00:34:43,659] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2515/markers.fasta)
[2023-03-16 00:34:43,660] [INFO] Task started: Blastn
[2023-03-16 00:34:43,660] [INFO] Running command: blastn -query OceanDNA-b2515/markers.fasta -db /var/lib/cwl/stg97d82199-989b-4851-bbfd-c1ff28f52039/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2515/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:34:44,510] [INFO] Task succeeded: Blastn
[2023-03-16 00:34:44,511] [INFO] Selected 19 target genomes.
[2023-03-16 00:34:44,511] [INFO] Target genome list was writen to OceanDNA-b2515/target_genomes_gtdb.txt
[2023-03-16 00:34:44,699] [INFO] Task started: fastANI
[2023-03-16 00:34:44,699] [INFO] Running command: fastANI --query /var/lib/cwl/stg85370f69-6d24-4cb4-8dd0-49cd6dfdf487/OceanDNA-b2515.fa --refList OceanDNA-b2515/target_genomes_gtdb.txt --output OceanDNA-b2515/fastani_result_gtdb.tsv --threads 1
[2023-03-16 00:34:59,707] [INFO] Task succeeded: fastANI
[2023-03-16 00:34:59,719] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 00:34:59,719] [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_003053885.1	s__Nocardioides sp003053885	76.3799	66	250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805845.1	s__Marmoricola_A sp902805845	76.3357	59	250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111455.1	s__Geodermatophilus poikilotrophus	76.3244	132	250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011250645.1	s__Motilibacter_A aurantiacus	76.2619	117	250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Motilibacterales;f__Motilibacteraceae;g__Motilibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129495.1	s__Geodermatophilus nigrescens	76.2504	151	250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216915.1	s__Motilibacter rhizosphaerae	76.1294	120	250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Motilibacterales;f__Motilibacteraceae;g__Motilibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409425.1	s__Nocardioides perillae	76.1144	121	250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806005.1	s__Quadrisphaera sp902806005	76.0129	83	250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Quadrisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011250635.1	s__Motilibacter_A deserti	76.0051	111	250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Motilibacterales;f__Motilibacteraceae;g__Motilibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805565.1	s__CADCTP01 sp902805565	75.9787	108	250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__CADCTP01;g__CADCTP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015390235.1	s__Quadrisphaera sp015390235	75.8549	113	250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Quadrisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001854805.1	s__Frankia sp001854805	75.846	128	250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000235425.2	s__Frankia saprophytica	75.8456	122	250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia	95.0	99.94	99.94	1.00	1.00	2	-
GCF_002198675.1	s__R-H-3 sp002198675	75.8248	145	250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__R-H-3	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012034935.1	s__Streptomyces sp012034935	75.5814	96	250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001270745.1	s__Jiangella muralis	75.5573	130	250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000515395.1	s__Jiangella gansuensis	75.4781	96	250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202285.1	s__Saccharomonospora muralis	75.3979	110	250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016907755.1	s__Cellulosimicrobium cellulans_D	75.3115	112	250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	99.18	99.18	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-03-16 00:34:59,724] [INFO] GTDB search result was written to OceanDNA-b2515/result_gtdb.tsv
[2023-03-16 00:34:59,724] [INFO] ===== GTDB Search completed =====
[2023-03-16 00:34:59,726] [INFO] DFAST_QC result json was written to OceanDNA-b2515/dqc_result.json
[2023-03-16 00:34:59,726] [INFO] DFAST_QC completed!
[2023-03-16 00:34:59,726] [INFO] Total running time: 0h1m13s