[2024-01-25 17:51:35,629] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:51:35,631] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:51:35,631] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c64b913-53d5-483d-a02e-cac82948379f/dqc_reference
[2024-01-25 17:51:36,768] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:51:36,781] [INFO] Task started: Prodigal
[2024-01-25 17:51:36,782] [INFO] Running command: gunzip -c /var/lib/cwl/stg474d1318-8319-48a7-952a-7f806cfdb78f/GCF_000012905.2_ASM1290v2_genomic.fna.gz | prodigal -d GCF_000012905.2_ASM1290v2_genomic.fna/cds.fna -a GCF_000012905.2_ASM1290v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:51:48,104] [INFO] Task succeeded: Prodigal
[2024-01-25 17:51:48,104] [INFO] Task started: HMMsearch
[2024-01-25 17:51:48,104] [INFO] Running command: hmmsearch --tblout GCF_000012905.2_ASM1290v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c64b913-53d5-483d-a02e-cac82948379f/dqc_reference/reference_markers.hmm GCF_000012905.2_ASM1290v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:51:48,377] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:51:48,380] [INFO] Found 6/6 markers.
[2024-01-25 17:51:48,426] [INFO] Query marker FASTA was written to GCF_000012905.2_ASM1290v2_genomic.fna/markers.fasta
[2024-01-25 17:51:48,426] [INFO] Task started: Blastn
[2024-01-25 17:51:48,426] [INFO] Running command: blastn -query GCF_000012905.2_ASM1290v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c64b913-53d5-483d-a02e-cac82948379f/dqc_reference/reference_markers.fasta -out GCF_000012905.2_ASM1290v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:51:49,503] [INFO] Task succeeded: Blastn
[2024-01-25 17:51:49,506] [INFO] Selected 10 target genomes.
[2024-01-25 17:51:49,506] [INFO] Target genome list was writen to GCF_000012905.2_ASM1290v2_genomic.fna/target_genomes.txt
[2024-01-25 17:51:49,516] [INFO] Task started: fastANI
[2024-01-25 17:51:49,516] [INFO] Running command: fastANI --query /var/lib/cwl/stg474d1318-8319-48a7-952a-7f806cfdb78f/GCF_000012905.2_ASM1290v2_genomic.fna.gz --refList GCF_000012905.2_ASM1290v2_genomic.fna/target_genomes.txt --output GCF_000012905.2_ASM1290v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:52:00,939] [INFO] Task succeeded: fastANI
[2024-01-25 17:52:00,939] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c64b913-53d5-483d-a02e-cac82948379f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:52:00,939] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c64b913-53d5-483d-a02e-cac82948379f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:52:00,947] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-25 17:52:00,947] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:52:00,947] [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
Cereibacter sphaeroides	strain=2.4.1	GCA_000012905.2	1063	1063	type	True	100.0	1532	1532	95	conclusive
Cereibacter sphaeroides	strain=2.4.1	GCA_000273405.1	1063	1063	type	True	99.9973	1528	1532	95	conclusive
Cereibacter sphaeroides	strain=2.4.1	GCA_000269625.2	1063	1063	type	True	99.9951	1525	1532	95	conclusive
Cereibacter sphaeroides	strain=2.4.1	GCA_003324715.1	1063	1063	type	True	99.9916	1528	1532	95	conclusive
Cereibacter sphaeroides	strain=NBRC 12203	GCA_007991035.1	1063	1063	type	True	99.9507	1456	1532	95	conclusive
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	87.1523	1009	1532	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	87.0866	1059	1532	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	82.8242	822	1532	95	below_threshold
Rhodobacter calidifons	strain=M37P	GCA_011174775.1	2715277	2715277	type	True	79.2502	558	1532	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	78.6383	517	1532	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:52:00,948] [INFO] DFAST Taxonomy check result was written to GCF_000012905.2_ASM1290v2_genomic.fna/tc_result.tsv
[2024-01-25 17:52:00,949] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:52:00,949] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:52:00,949] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c64b913-53d5-483d-a02e-cac82948379f/dqc_reference/checkm_data
[2024-01-25 17:52:00,950] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:52:00,992] [INFO] Task started: CheckM
[2024-01-25 17:52:00,992] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000012905.2_ASM1290v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000012905.2_ASM1290v2_genomic.fna/checkm_input GCF_000012905.2_ASM1290v2_genomic.fna/checkm_result
[2024-01-25 17:52:58,179] [INFO] Task succeeded: CheckM
[2024-01-25 17:52:58,180] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:52:58,197] [INFO] ===== Completeness check finished =====
[2024-01-25 17:52:58,198] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:52:58,199] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000012905.2_ASM1290v2_genomic.fna/markers.fasta)
[2024-01-25 17:52:58,199] [INFO] Task started: Blastn
[2024-01-25 17:52:58,199] [INFO] Running command: blastn -query GCF_000012905.2_ASM1290v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c64b913-53d5-483d-a02e-cac82948379f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000012905.2_ASM1290v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:53:00,323] [INFO] Task succeeded: Blastn
[2024-01-25 17:53:00,325] [INFO] Selected 6 target genomes.
[2024-01-25 17:53:00,325] [INFO] Target genome list was writen to GCF_000012905.2_ASM1290v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:53:00,329] [INFO] Task started: fastANI
[2024-01-25 17:53:00,329] [INFO] Running command: fastANI --query /var/lib/cwl/stg474d1318-8319-48a7-952a-7f806cfdb78f/GCF_000012905.2_ASM1290v2_genomic.fna.gz --refList GCF_000012905.2_ASM1290v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000012905.2_ASM1290v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:53:07,183] [INFO] Task succeeded: fastANI
[2024-01-25 17:53:07,188] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:53:07,188] [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_000012905.2	s__Cereibacter_A sphaeroides	100.0	1531	1532	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.1736	98.82	96.57	0.94	0.87	24	conclusive
GCF_001720585.1	s__Cereibacter_A johrii	95.1519	1154	1532	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.1736	98.42	97.86	0.94	0.91	6	-
GCA_017599285.1	s__Cereibacter_A azotoformans	87.5356	885	1532	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.0	98.54	95.54	0.92	0.86	6	-
GCF_002407205.1	s__Cereibacter_A sp002407205	84.8536	1014	1532	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900207575.1	s__Cereibacter_A ovatus	82.7939	825	1532	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034985.1	s__Cereibacter changlensis	82.5171	818	1532	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter	95.0	98.07	96.18	0.89	0.78	3	-
--------------------------------------------------------------------------------
[2024-01-25 17:53:07,189] [INFO] GTDB search result was written to GCF_000012905.2_ASM1290v2_genomic.fna/result_gtdb.tsv
[2024-01-25 17:53:07,190] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:53:07,193] [INFO] DFAST_QC result json was written to GCF_000012905.2_ASM1290v2_genomic.fna/dqc_result.json
[2024-01-25 17:53:07,193] [INFO] DFAST_QC completed!
[2024-01-25 17:53:07,194] [INFO] Total running time: 0h1m32s