[2023-06-17 12:34:52,606] [INFO] DFAST_QC pipeline started.
[2023-06-17 12:34:52,609] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 12:34:52,610] [INFO] DQC Reference Directory: /var/lib/cwl/stg663bd315-0091-454e-9907-14e1a65b1ae6/dqc_reference
[2023-06-17 12:34:53,786] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 12:34:53,787] [INFO] Task started: Prodigal
[2023-06-17 12:34:53,787] [INFO] Running command: gunzip -c /var/lib/cwl/stgdb8f29c9-5511-458f-a86c-fd18c79911dc/GCA_013335795.1_ASM1333579v1_genomic.fna.gz | prodigal -d GCA_013335795.1_ASM1333579v1_genomic.fna/cds.fna -a GCA_013335795.1_ASM1333579v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 12:35:04,137] [INFO] Task succeeded: Prodigal
[2023-06-17 12:35:04,138] [INFO] Task started: HMMsearch
[2023-06-17 12:35:04,138] [INFO] Running command: hmmsearch --tblout GCA_013335795.1_ASM1333579v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg663bd315-0091-454e-9907-14e1a65b1ae6/dqc_reference/reference_markers.hmm GCA_013335795.1_ASM1333579v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 12:35:04,308] [INFO] Task succeeded: HMMsearch
[2023-06-17 12:35:04,310] [INFO] Found 6/6 markers.
[2023-06-17 12:35:04,331] [INFO] Query marker FASTA was written to GCA_013335795.1_ASM1333579v1_genomic.fna/markers.fasta
[2023-06-17 12:35:04,332] [INFO] Task started: Blastn
[2023-06-17 12:35:04,332] [INFO] Running command: blastn -query GCA_013335795.1_ASM1333579v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg663bd315-0091-454e-9907-14e1a65b1ae6/dqc_reference/reference_markers.fasta -out GCA_013335795.1_ASM1333579v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 12:35:04,888] [INFO] Task succeeded: Blastn
[2023-06-17 12:35:04,892] [INFO] Selected 16 target genomes.
[2023-06-17 12:35:04,893] [INFO] Target genome list was writen to GCA_013335795.1_ASM1333579v1_genomic.fna/target_genomes.txt
[2023-06-17 12:35:04,894] [INFO] Task started: fastANI
[2023-06-17 12:35:04,895] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb8f29c9-5511-458f-a86c-fd18c79911dc/GCA_013335795.1_ASM1333579v1_genomic.fna.gz --refList GCA_013335795.1_ASM1333579v1_genomic.fna/target_genomes.txt --output GCA_013335795.1_ASM1333579v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 12:35:12,675] [INFO] Task succeeded: fastANI
[2023-06-17 12:35:12,675] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg663bd315-0091-454e-9907-14e1a65b1ae6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 12:35:12,675] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg663bd315-0091-454e-9907-14e1a65b1ae6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 12:35:12,682] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 12:35:12,682] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 12:35:12,682] [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
Pelodictyon phaeoclathratiforme	strain=BU-1	GCA_000020645.1	34090	34090	type	True	81.4355	417	626	95	below_threshold
Chlorobium ferrooxidans	strain=DSM 13031	GCA_000168715.1	84205	84205	type	True	78.2612	260	626	95	below_threshold
Chlorobium limicola	strain=DSM 245	GCA_000020465.1	1092	1092	type	True	77.3879	104	626	95	below_threshold
Chlorobium phaeobacteroides	strain=DSM 266	GCA_000015125.1	1096	1096	type	True	77.2651	133	626	95	below_threshold
Pelodictyon luteolum	strain=DSM 273	GCA_000012485.1	1100	1100	type	True	76.7042	57	626	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 12:35:12,684] [INFO] DFAST Taxonomy check result was written to GCA_013335795.1_ASM1333579v1_genomic.fna/tc_result.tsv
[2023-06-17 12:35:12,685] [INFO] ===== Taxonomy check completed =====
[2023-06-17 12:35:12,685] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 12:35:12,685] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg663bd315-0091-454e-9907-14e1a65b1ae6/dqc_reference/checkm_data
[2023-06-17 12:35:12,686] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 12:35:12,712] [INFO] Task started: CheckM
[2023-06-17 12:35:12,712] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013335795.1_ASM1333579v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013335795.1_ASM1333579v1_genomic.fna/checkm_input GCA_013335795.1_ASM1333579v1_genomic.fna/checkm_result
[2023-06-17 12:35:49,449] [INFO] Task succeeded: CheckM
[2023-06-17 12:35:49,451] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.99%
Contamintation: 0.98%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-17 12:35:49,469] [INFO] ===== Completeness check finished =====
[2023-06-17 12:35:49,470] [INFO] ===== Start GTDB Search =====
[2023-06-17 12:35:49,470] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013335795.1_ASM1333579v1_genomic.fna/markers.fasta)
[2023-06-17 12:35:49,470] [INFO] Task started: Blastn
[2023-06-17 12:35:49,470] [INFO] Running command: blastn -query GCA_013335795.1_ASM1333579v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg663bd315-0091-454e-9907-14e1a65b1ae6/dqc_reference/reference_markers_gtdb.fasta -out GCA_013335795.1_ASM1333579v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 12:35:50,273] [INFO] Task succeeded: Blastn
[2023-06-17 12:35:50,277] [INFO] Selected 12 target genomes.
[2023-06-17 12:35:50,277] [INFO] Target genome list was writen to GCA_013335795.1_ASM1333579v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 12:35:50,287] [INFO] Task started: fastANI
[2023-06-17 12:35:50,287] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb8f29c9-5511-458f-a86c-fd18c79911dc/GCA_013335795.1_ASM1333579v1_genomic.fna.gz --refList GCA_013335795.1_ASM1333579v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013335795.1_ASM1333579v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 12:35:55,911] [INFO] Task succeeded: fastANI
[2023-06-17 12:35:55,921] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 12:35:55,921] [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_013334755.1	s__Chlorobium sp013334755	99.5967	553	626	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.60	99.60	0.88	0.88	2	conclusive
GCA_903822595.1	s__Chlorobium sp903822595	81.7521	409	626	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.84	99.77	0.94	0.93	3	-
GCA_903820085.1	s__Chlorobium sp903820085	81.6812	404	626	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.98	99.89	0.98	0.91	15	-
GCA_903882665.1	s__Chlorobium sp903882665	81.4979	409	626	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.16	98.83	0.90	0.84	7	-
GCF_000020645.1	s__Chlorobium phaeoclathratiforme	81.4518	416	626	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.98	99.98	1.00	1.00	2	-
GCA_903865705.1	s__Chlorobium sp903865705	81.4204	343	626	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.47	99.06	0.91	0.87	5	-
GCA_903840935.1	s__Chlorobium sp903840935	81.0742	336	626	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.22	98.87	0.67	0.63	5	-
GCA_903824295.1	s__Chlorobium sp903824295	80.8638	369	626	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.79	99.65	0.92	0.89	3	-
GCA_903887845.1	s__Chlorobium sp903887845	79.8488	311	626	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.96	99.96	0.95	0.95	2	-
GCA_903836465.1	s__Chlorobium sp903836465	79.6642	321	626	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.30	97.63	0.95	0.90	12	-
GCA_903994525.1	s__Chlorobium sp903994525	77.8752	194	626	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.83	98.94	0.92	0.84	27	-
GCA_013336025.1	s__Chlorobium sp013336025	77.3326	93	626	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 12:35:55,923] [INFO] GTDB search result was written to GCA_013335795.1_ASM1333579v1_genomic.fna/result_gtdb.tsv
[2023-06-17 12:35:55,924] [INFO] ===== GTDB Search completed =====
[2023-06-17 12:35:55,927] [INFO] DFAST_QC result json was written to GCA_013335795.1_ASM1333579v1_genomic.fna/dqc_result.json
[2023-06-17 12:35:55,927] [INFO] DFAST_QC completed!
[2023-06-17 12:35:55,927] [INFO] Total running time: 0h1m3s