[2023-06-29 04:41:50,047] [INFO] DFAST_QC pipeline started.
[2023-06-29 04:41:50,049] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 04:41:50,049] [INFO] DQC Reference Directory: /var/lib/cwl/stgdeaf924c-2cda-4def-aa17-0b7d736963a9/dqc_reference
[2023-06-29 04:41:51,247] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 04:41:51,248] [INFO] Task started: Prodigal
[2023-06-29 04:41:51,248] [INFO] Running command: gunzip -c /var/lib/cwl/stgb2bc79a4-13eb-44f8-97ca-30a372592766/GCA_027395015.1_ASM2739501v1_genomic.fna.gz | prodigal -d GCA_027395015.1_ASM2739501v1_genomic.fna/cds.fna -a GCA_027395015.1_ASM2739501v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 04:41:53,883] [INFO] Task succeeded: Prodigal
[2023-06-29 04:41:53,883] [INFO] Task started: HMMsearch
[2023-06-29 04:41:53,884] [INFO] Running command: hmmsearch --tblout GCA_027395015.1_ASM2739501v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdeaf924c-2cda-4def-aa17-0b7d736963a9/dqc_reference/reference_markers.hmm GCA_027395015.1_ASM2739501v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 04:41:54,041] [INFO] Task succeeded: HMMsearch
[2023-06-29 04:41:54,042] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgb2bc79a4-13eb-44f8-97ca-30a372592766/GCA_027395015.1_ASM2739501v1_genomic.fna.gz]
[2023-06-29 04:41:54,055] [INFO] Query marker FASTA was written to GCA_027395015.1_ASM2739501v1_genomic.fna/markers.fasta
[2023-06-29 04:41:54,056] [INFO] Task started: Blastn
[2023-06-29 04:41:54,056] [INFO] Running command: blastn -query GCA_027395015.1_ASM2739501v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdeaf924c-2cda-4def-aa17-0b7d736963a9/dqc_reference/reference_markers.fasta -out GCA_027395015.1_ASM2739501v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 04:41:54,576] [INFO] Task succeeded: Blastn
[2023-06-29 04:41:54,579] [INFO] Selected 15 target genomes.
[2023-06-29 04:41:54,579] [INFO] Target genome list was writen to GCA_027395015.1_ASM2739501v1_genomic.fna/target_genomes.txt
[2023-06-29 04:41:54,582] [INFO] Task started: fastANI
[2023-06-29 04:41:54,582] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2bc79a4-13eb-44f8-97ca-30a372592766/GCA_027395015.1_ASM2739501v1_genomic.fna.gz --refList GCA_027395015.1_ASM2739501v1_genomic.fna/target_genomes.txt --output GCA_027395015.1_ASM2739501v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 04:42:06,641] [INFO] Task succeeded: fastANI
[2023-06-29 04:42:06,641] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdeaf924c-2cda-4def-aa17-0b7d736963a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 04:42:06,641] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdeaf924c-2cda-4def-aa17-0b7d736963a9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 04:42:06,648] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 04:42:06,648] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 04:42:06,648] [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
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.1998	62	314	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	75.4962	59	314	95	below_threshold
Nonomuraea ceibae	strain=KCTC 39826	GCA_019396325.1	1935170	1935170	type	True	75.2065	59	314	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 04:42:06,650] [INFO] DFAST Taxonomy check result was written to GCA_027395015.1_ASM2739501v1_genomic.fna/tc_result.tsv
[2023-06-29 04:42:06,651] [INFO] ===== Taxonomy check completed =====
[2023-06-29 04:42:06,651] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 04:42:06,651] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdeaf924c-2cda-4def-aa17-0b7d736963a9/dqc_reference/checkm_data
[2023-06-29 04:42:06,653] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 04:42:06,667] [INFO] Task started: CheckM
[2023-06-29 04:42:06,667] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027395015.1_ASM2739501v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027395015.1_ASM2739501v1_genomic.fna/checkm_input GCA_027395015.1_ASM2739501v1_genomic.fna/checkm_result
[2023-06-29 04:42:21,166] [INFO] Task succeeded: CheckM
[2023-06-29 04:42:21,168] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 29.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 04:42:21,182] [INFO] ===== Completeness check finished =====
[2023-06-29 04:42:21,182] [INFO] ===== Start GTDB Search =====
[2023-06-29 04:42:21,183] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027395015.1_ASM2739501v1_genomic.fna/markers.fasta)
[2023-06-29 04:42:21,183] [INFO] Task started: Blastn
[2023-06-29 04:42:21,183] [INFO] Running command: blastn -query GCA_027395015.1_ASM2739501v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdeaf924c-2cda-4def-aa17-0b7d736963a9/dqc_reference/reference_markers_gtdb.fasta -out GCA_027395015.1_ASM2739501v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 04:42:21,732] [INFO] Task succeeded: Blastn
[2023-06-29 04:42:21,735] [INFO] Selected 13 target genomes.
[2023-06-29 04:42:21,736] [INFO] Target genome list was writen to GCA_027395015.1_ASM2739501v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 04:42:21,737] [INFO] Task started: fastANI
[2023-06-29 04:42:21,737] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2bc79a4-13eb-44f8-97ca-30a372592766/GCA_027395015.1_ASM2739501v1_genomic.fna.gz --refList GCA_027395015.1_ASM2739501v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027395015.1_ASM2739501v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 04:42:26,858] [INFO] Task succeeded: fastANI
[2023-06-29 04:42:26,870] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 04:42:26,870] [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_001443545.1	s__RAAP-2 sp001443545	81.3464	215	314	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017883045.1	s__RAAP-2 sp017883045	79.5991	153	314	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003138815.1	s__RAAP-2 sp003138815	79.4644	152	314	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	99.85	99.69	0.94	0.86	28	-
GCA_903860745.1	s__RAAP-2 sp903860745	79.1249	135	314	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	99.88	99.81	0.92	0.91	5	-
GCA_002255565.1	s__RAAP-2 sp002255565	79.0671	151	314	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018971185.1	s__RAAP-2 sp018971185	78.5486	128	314	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003158855.1	s__RAAP-2 sp003158855	78.133	128	314	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882985.1	s__RAAP-2 sp017882985	77.9817	66	314	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003141815.1	s__RAAP-2 sp003141815	77.619	90	314	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003134515.1	s__RAAP-2 sp003134515	77.3666	86	314	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003132305.1	s__RAAP-2 sp003132305	77.1494	116	314	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	99.85	99.79	0.98	0.97	7	-
GCA_003155135.1	s__Bog-515 sp003155135	77.1363	63	314	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__Bog-515	95.0	99.89	99.76	0.97	0.95	17	-
GCA_003151555.1	s__RAAP-2 sp003151555	77.0518	84	314	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__RAAP-2;g__RAAP-2	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 04:42:26,872] [INFO] GTDB search result was written to GCA_027395015.1_ASM2739501v1_genomic.fna/result_gtdb.tsv
[2023-06-29 04:42:26,873] [INFO] ===== GTDB Search completed =====
[2023-06-29 04:42:26,876] [INFO] DFAST_QC result json was written to GCA_027395015.1_ASM2739501v1_genomic.fna/dqc_result.json
[2023-06-29 04:42:26,876] [INFO] DFAST_QC completed!
[2023-06-29 04:42:26,876] [INFO] Total running time: 0h0m37s