[2024-01-24 11:26:20,971] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:20,972] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:20,973] [INFO] DQC Reference Directory: /var/lib/cwl/stg4fbd5f03-f1cb-4c1f-9121-51dc99a2d4bb/dqc_reference
[2024-01-24 11:26:22,189] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:22,190] [INFO] Task started: Prodigal
[2024-01-24 11:26:22,190] [INFO] Running command: gunzip -c /var/lib/cwl/stg4c391552-1261-4d2c-b1c6-23749b4e3a62/GCF_014192155.1_ASM1419215v1_genomic.fna.gz | prodigal -d GCF_014192155.1_ASM1419215v1_genomic.fna/cds.fna -a GCF_014192155.1_ASM1419215v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:40,982] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:40,983] [INFO] Task started: HMMsearch
[2024-01-24 11:26:40,983] [INFO] Running command: hmmsearch --tblout GCF_014192155.1_ASM1419215v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4fbd5f03-f1cb-4c1f-9121-51dc99a2d4bb/dqc_reference/reference_markers.hmm GCF_014192155.1_ASM1419215v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:41,372] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:41,374] [INFO] Found 6/6 markers.
[2024-01-24 11:26:41,425] [INFO] Query marker FASTA was written to GCF_014192155.1_ASM1419215v1_genomic.fna/markers.fasta
[2024-01-24 11:26:41,425] [INFO] Task started: Blastn
[2024-01-24 11:26:41,425] [INFO] Running command: blastn -query GCF_014192155.1_ASM1419215v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4fbd5f03-f1cb-4c1f-9121-51dc99a2d4bb/dqc_reference/reference_markers.fasta -out GCF_014192155.1_ASM1419215v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:42,406] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:42,410] [INFO] Selected 17 target genomes.
[2024-01-24 11:26:42,411] [INFO] Target genome list was writen to GCF_014192155.1_ASM1419215v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:42,417] [INFO] Task started: fastANI
[2024-01-24 11:26:42,417] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c391552-1261-4d2c-b1c6-23749b4e3a62/GCF_014192155.1_ASM1419215v1_genomic.fna.gz --refList GCF_014192155.1_ASM1419215v1_genomic.fna/target_genomes.txt --output GCF_014192155.1_ASM1419215v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:00,333] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:00,334] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4fbd5f03-f1cb-4c1f-9121-51dc99a2d4bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:00,335] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4fbd5f03-f1cb-4c1f-9121-51dc99a2d4bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:00,351] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:00,351] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:00,351] [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
Roseateles terrae	strain=CECT 7247	GCA_014192155.1	431060	431060	type	True	100.0	1827	1828	95	conclusive
Roseateles depolymerans	strain=DSM 11813	GCA_003387155.1	76731	76731	type	True	87.1397	1529	1828	95	below_threshold
Mitsuaria chitinivorans	strain=HWN-4	GCA_002761755.1	2917965	2917965	type	True	82.1758	1070	1828	95	below_threshold
Pelomonas saccharophila	strain=DSM 654	GCA_004342485.1	304	304	type	True	79.8264	673	1828	95	below_threshold
Pelomonas puraquae	strain=CCUG 52769	GCA_002205845.1	431059	431059	type	True	79.6857	726	1828	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	79.6204	534	1828	95	below_threshold
Ideonella azotifigens	strain=DSM 21438	GCA_006519715.1	513160	513160	type	True	79.4548	510	1828	95	below_threshold
Paucibacter toxinivorans	strain=DSM 16998	GCA_004362525.1	270368	270368	type	True	79.1585	679	1828	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	79.1556	538	1828	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	79.0866	497	1828	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	79.0447	520	1828	95	below_threshold
Azohydromonas lata	strain=NBRC 102462	GCA_001571085.1	45677	45677	type	True	78.9649	517	1828	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	78.8273	522	1828	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	78.6219	564	1828	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	78.3816	457	1828	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	78.3745	518	1828	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	78.2794	468	1828	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:00,353] [INFO] DFAST Taxonomy check result was written to GCF_014192155.1_ASM1419215v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:00,353] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:00,353] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:00,353] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4fbd5f03-f1cb-4c1f-9121-51dc99a2d4bb/dqc_reference/checkm_data
[2024-01-24 11:27:00,354] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:00,414] [INFO] Task started: CheckM
[2024-01-24 11:27:00,415] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014192155.1_ASM1419215v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014192155.1_ASM1419215v1_genomic.fna/checkm_input GCF_014192155.1_ASM1419215v1_genomic.fna/checkm_result
[2024-01-24 11:28:40,075] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:40,076] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:40,100] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:40,100] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:40,101] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014192155.1_ASM1419215v1_genomic.fna/markers.fasta)
[2024-01-24 11:28:40,101] [INFO] Task started: Blastn
[2024-01-24 11:28:40,101] [INFO] Running command: blastn -query GCF_014192155.1_ASM1419215v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4fbd5f03-f1cb-4c1f-9121-51dc99a2d4bb/dqc_reference/reference_markers_gtdb.fasta -out GCF_014192155.1_ASM1419215v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:41,979] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:41,984] [INFO] Selected 11 target genomes.
[2024-01-24 11:28:41,984] [INFO] Target genome list was writen to GCF_014192155.1_ASM1419215v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:41,997] [INFO] Task started: fastANI
[2024-01-24 11:28:41,997] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c391552-1261-4d2c-b1c6-23749b4e3a62/GCF_014192155.1_ASM1419215v1_genomic.fna.gz --refList GCF_014192155.1_ASM1419215v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014192155.1_ASM1419215v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:55,994] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:56,007] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:56,007] [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_014192155.1	s__Roseateles terrae	100.0	1827	1828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Roseateles	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003387155.1	s__Roseateles depolymerans	87.1462	1528	1828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Roseateles	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900109745.1	s__Roseateles sp900109745	84.042	1272	1828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Roseateles	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598255.1	s__Mitsuaria chitosanitabida	82.3125	1093	1828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	99.05	99.05	0.96	0.96	2	-
GCF_900113225.1	s__Mitsuaria sp900113225	82.2801	1127	1828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	98.36	98.28	0.95	0.95	4	-
GCF_002761755.1	s__Mitsuaria sp002761755	82.1969	1067	1828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002205645.1	s__Mitsuaria aquatilis	82.1238	1079	1828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002205125.1	s__Mitsuaria noduli	81.6432	1107	1828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004210455.1	s__Mitsuaria sp004210455	81.5952	1046	1828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001653795.1	s__Mitsuaria sp001653795	81.5284	1004	1828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362405.1	s__Kinneretia asaccharophila	80.3545	688	1828	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Kinneretia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:56,008] [INFO] GTDB search result was written to GCF_014192155.1_ASM1419215v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:56,009] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:56,012] [INFO] DFAST_QC result json was written to GCF_014192155.1_ASM1419215v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:56,012] [INFO] DFAST_QC completed!
[2024-01-24 11:28:56,012] [INFO] Total running time: 0h2m35s