[2023-06-04 18:59:07,675] [INFO] DFAST_QC pipeline started.
[2023-06-04 18:59:07,697] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 18:59:07,697] [INFO] DQC Reference Directory: /var/lib/cwl/stg670cfc42-a25f-45a9-90f3-d58a6d82d30f/dqc_reference
[2023-06-04 18:59:10,194] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 18:59:10,195] [INFO] Task started: Prodigal
[2023-06-04 18:59:10,195] [INFO] Running command: gunzip -c /var/lib/cwl/stg43ddeb3c-0980-49b0-820e-4f97a3c0357a/GCA_934129745.1_ERR7738195_bin.52_genomic.fna.gz | prodigal -d GCA_934129745.1_ERR7738195_bin.52_genomic.fna/cds.fna -a GCA_934129745.1_ERR7738195_bin.52_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 18:59:13,154] [INFO] Task succeeded: Prodigal
[2023-06-04 18:59:13,154] [INFO] Task started: HMMsearch
[2023-06-04 18:59:13,155] [INFO] Running command: hmmsearch --tblout GCA_934129745.1_ERR7738195_bin.52_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg670cfc42-a25f-45a9-90f3-d58a6d82d30f/dqc_reference/reference_markers.hmm GCA_934129745.1_ERR7738195_bin.52_genomic.fna/protein.faa > /dev/null
[2023-06-04 18:59:13,386] [INFO] Task succeeded: HMMsearch
[2023-06-04 18:59:13,388] [INFO] Found 6/6 markers.
[2023-06-04 18:59:13,412] [INFO] Query marker FASTA was written to GCA_934129745.1_ERR7738195_bin.52_genomic.fna/markers.fasta
[2023-06-04 18:59:13,412] [INFO] Task started: Blastn
[2023-06-04 18:59:13,413] [INFO] Running command: blastn -query GCA_934129745.1_ERR7738195_bin.52_genomic.fna/markers.fasta -db /var/lib/cwl/stg670cfc42-a25f-45a9-90f3-d58a6d82d30f/dqc_reference/reference_markers.fasta -out GCA_934129745.1_ERR7738195_bin.52_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 18:59:15,190] [INFO] Task succeeded: Blastn
[2023-06-04 18:59:15,195] [INFO] Selected 21 target genomes.
[2023-06-04 18:59:15,196] [INFO] Target genome list was writen to GCA_934129745.1_ERR7738195_bin.52_genomic.fna/target_genomes.txt
[2023-06-04 18:59:15,246] [INFO] Task started: fastANI
[2023-06-04 18:59:15,246] [INFO] Running command: fastANI --query /var/lib/cwl/stg43ddeb3c-0980-49b0-820e-4f97a3c0357a/GCA_934129745.1_ERR7738195_bin.52_genomic.fna.gz --refList GCA_934129745.1_ERR7738195_bin.52_genomic.fna/target_genomes.txt --output GCA_934129745.1_ERR7738195_bin.52_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 18:59:25,005] [INFO] Task succeeded: fastANI
[2023-06-04 18:59:25,006] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg670cfc42-a25f-45a9-90f3-d58a6d82d30f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 18:59:25,006] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg670cfc42-a25f-45a9-90f3-d58a6d82d30f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 18:59:25,019] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 18:59:25,019] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 18:59:25,019] [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
Clostridium uliginosum	strain=DSM 12992	GCA_900112485.1	119641	119641	type	True	74.9557	55	592	95	below_threshold
Clostridium tetanomorphum	strain=DSM 4474	GCA_017873215.1	1553	1553	type	True	74.9354	53	592	95	below_threshold
Clostridioides difficile	strain=ATCC 9689	GCA_000376285.1	1496	1496	type	True	74.9135	55	592	95	below_threshold
Clostridioides difficile	strain=DSM 1296	GCA_000438845.1	1496	1496	type	True	74.8995	57	592	95	below_threshold
Clostridium massiliamazoniense	strain=ND2	GCA_001403635.1	1347366	1347366	type	True	74.8354	53	592	95	below_threshold
Paraclostridium bifermentans	strain=ATCC 638	GCA_000452245.2	1490	1490	type	True	74.7441	55	592	95	below_threshold
Paraclostridium bifermentans	strain=DSM 14991	GCA_019916025.1	1490	1490	type	True	74.7438	54	592	95	below_threshold
Paraclostridium dentum	strain=SKVG24	GCA_012922555.1	2662455	2662455	type	True	74.7254	54	592	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 18:59:25,021] [INFO] DFAST Taxonomy check result was written to GCA_934129745.1_ERR7738195_bin.52_genomic.fna/tc_result.tsv
[2023-06-04 18:59:25,022] [INFO] ===== Taxonomy check completed =====
[2023-06-04 18:59:25,022] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 18:59:25,023] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg670cfc42-a25f-45a9-90f3-d58a6d82d30f/dqc_reference/checkm_data
[2023-06-04 18:59:25,025] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 18:59:25,047] [INFO] Task started: CheckM
[2023-06-04 18:59:25,047] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934129745.1_ERR7738195_bin.52_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934129745.1_ERR7738195_bin.52_genomic.fna/checkm_input GCA_934129745.1_ERR7738195_bin.52_genomic.fna/checkm_result
[2023-06-04 18:59:41,720] [INFO] Task succeeded: CheckM
[2023-06-04 18:59:41,722] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 18:59:41,742] [INFO] ===== Completeness check finished =====
[2023-06-04 18:59:41,743] [INFO] ===== Start GTDB Search =====
[2023-06-04 18:59:41,743] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934129745.1_ERR7738195_bin.52_genomic.fna/markers.fasta)
[2023-06-04 18:59:41,744] [INFO] Task started: Blastn
[2023-06-04 18:59:41,744] [INFO] Running command: blastn -query GCA_934129745.1_ERR7738195_bin.52_genomic.fna/markers.fasta -db /var/lib/cwl/stg670cfc42-a25f-45a9-90f3-d58a6d82d30f/dqc_reference/reference_markers_gtdb.fasta -out GCA_934129745.1_ERR7738195_bin.52_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 18:59:42,557] [INFO] Task succeeded: Blastn
[2023-06-04 18:59:42,580] [INFO] Selected 15 target genomes.
[2023-06-04 18:59:42,580] [INFO] Target genome list was writen to GCA_934129745.1_ERR7738195_bin.52_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 18:59:42,672] [INFO] Task started: fastANI
[2023-06-04 18:59:42,672] [INFO] Running command: fastANI --query /var/lib/cwl/stg43ddeb3c-0980-49b0-820e-4f97a3c0357a/GCA_934129745.1_ERR7738195_bin.52_genomic.fna.gz --refList GCA_934129745.1_ERR7738195_bin.52_genomic.fna/target_genomes_gtdb.txt --output GCA_934129745.1_ERR7738195_bin.52_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 18:59:47,228] [INFO] Task succeeded: fastANI
[2023-06-04 18:59:47,245] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-04 18:59:47,246] [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_017475185.1	s__CAG-492 sp017475185	82.1069	277	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-492	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900557045.1	s__CAG-492 sp900557045	81.7844	269	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-492	95.0	99.42	99.42	0.77	0.77	2	-
GCA_017528375.1	s__CAG-492 sp017528375	81.494	268	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-492	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017470645.1	s__CAG-492 sp017470645	80.955	249	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-492	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002633185.1	s__CAG-492 sp002633185	80.0352	201	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-492	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000434015.1	s__CAG-492 sp000434015	78.6262	183	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-492	95.0	99.68	99.35	0.94	0.91	3	-
GCA_017937285.1	s__CAG-492 sp017937285	78.4354	201	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-492	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017626365.1	s__RGIG8482 sp017626365	78.1792	113	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__RGIG8482	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017404025.1	s__CAG-269 sp017404025	77.9357	157	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000437215.1	s__CAG-269 sp000437215	77.789	146	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	98.98	98.94	0.85	0.85	3	-
GCA_900554175.1	s__CAG-269 sp900554175	77.6007	113	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	99.99	99.99	0.98	0.96	3	-
GCA_017410505.1	s__CAG-269 sp017410505	77.3664	136	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900759475.1	s__UMGS1754 sp900759475	77.3113	100	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__UMGS1754	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900555615.1	s__CAG-269 sp900555615	77.1308	126	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	97.95	97.78	0.76	0.74	3	-
GCA_904419495.1	s__CAG-269 sp904419495	77.0164	121	592	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__CAG-269	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 18:59:47,248] [INFO] GTDB search result was written to GCA_934129745.1_ERR7738195_bin.52_genomic.fna/result_gtdb.tsv
[2023-06-04 18:59:47,248] [INFO] ===== GTDB Search completed =====
[2023-06-04 18:59:47,252] [INFO] DFAST_QC result json was written to GCA_934129745.1_ERR7738195_bin.52_genomic.fna/dqc_result.json
[2023-06-04 18:59:47,252] [INFO] DFAST_QC completed!
[2023-06-04 18:59:47,252] [INFO] Total running time: 0h0m40s