[2023-06-29 19:35:29,913] [INFO] DFAST_QC pipeline started.
[2023-06-29 19:35:29,915] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 19:35:29,916] [INFO] DQC Reference Directory: /var/lib/cwl/stg896d06cb-720c-467c-ba9d-9fdc91458dd7/dqc_reference
[2023-06-29 19:35:31,124] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 19:35:31,125] [INFO] Task started: Prodigal
[2023-06-29 19:35:31,126] [INFO] Running command: gunzip -c /var/lib/cwl/stgf148b16a-3801-45f4-a977-160e62e69d4d/GCA_023708705.1_ASM2370870v1_genomic.fna.gz | prodigal -d GCA_023708705.1_ASM2370870v1_genomic.fna/cds.fna -a GCA_023708705.1_ASM2370870v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 19:35:40,283] [INFO] Task succeeded: Prodigal
[2023-06-29 19:35:40,284] [INFO] Task started: HMMsearch
[2023-06-29 19:35:40,284] [INFO] Running command: hmmsearch --tblout GCA_023708705.1_ASM2370870v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg896d06cb-720c-467c-ba9d-9fdc91458dd7/dqc_reference/reference_markers.hmm GCA_023708705.1_ASM2370870v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 19:35:40,657] [INFO] Task succeeded: HMMsearch
[2023-06-29 19:35:40,659] [INFO] Found 6/6 markers.
[2023-06-29 19:35:40,695] [INFO] Query marker FASTA was written to GCA_023708705.1_ASM2370870v1_genomic.fna/markers.fasta
[2023-06-29 19:35:40,696] [INFO] Task started: Blastn
[2023-06-29 19:35:40,696] [INFO] Running command: blastn -query GCA_023708705.1_ASM2370870v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg896d06cb-720c-467c-ba9d-9fdc91458dd7/dqc_reference/reference_markers.fasta -out GCA_023708705.1_ASM2370870v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:35:41,361] [INFO] Task succeeded: Blastn
[2023-06-29 19:35:41,365] [INFO] Selected 26 target genomes.
[2023-06-29 19:35:41,366] [INFO] Target genome list was writen to GCA_023708705.1_ASM2370870v1_genomic.fna/target_genomes.txt
[2023-06-29 19:35:41,367] [INFO] Task started: fastANI
[2023-06-29 19:35:41,367] [INFO] Running command: fastANI --query /var/lib/cwl/stgf148b16a-3801-45f4-a977-160e62e69d4d/GCA_023708705.1_ASM2370870v1_genomic.fna.gz --refList GCA_023708705.1_ASM2370870v1_genomic.fna/target_genomes.txt --output GCA_023708705.1_ASM2370870v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 19:35:54,564] [INFO] Task succeeded: fastANI
[2023-06-29 19:35:54,565] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg896d06cb-720c-467c-ba9d-9fdc91458dd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 19:35:54,565] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg896d06cb-720c-467c-ba9d-9fdc91458dd7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 19:35:54,571] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 19:35:54,572] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 19:35:54,572] [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
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	83.6084	64	1014	95	below_threshold
Hydrogeniiclostridium mannosilyticum	strain=ASD2818	GCA_003268275.1	2764322	2764322	type	True	79.3038	55	1014	95	below_threshold
Anaeromassilibacillus senegalensis	strain=mt9	GCA_001261775.1	1673717	1673717	type	True	76.935	77	1014	95	below_threshold
Clostridium jeddahense	strain=JCD	GCA_000577335.1	1414721	1414721	type	True	76.6137	64	1014	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 19:35:54,574] [INFO] DFAST Taxonomy check result was written to GCA_023708705.1_ASM2370870v1_genomic.fna/tc_result.tsv
[2023-06-29 19:35:54,574] [INFO] ===== Taxonomy check completed =====
[2023-06-29 19:35:54,574] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 19:35:54,575] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg896d06cb-720c-467c-ba9d-9fdc91458dd7/dqc_reference/checkm_data
[2023-06-29 19:35:54,576] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 19:35:54,611] [INFO] Task started: CheckM
[2023-06-29 19:35:54,611] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023708705.1_ASM2370870v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023708705.1_ASM2370870v1_genomic.fna/checkm_input GCA_023708705.1_ASM2370870v1_genomic.fna/checkm_result
[2023-06-29 19:36:26,546] [INFO] Task succeeded: CheckM
[2023-06-29 19:36:26,547] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 19:36:26,570] [INFO] ===== Completeness check finished =====
[2023-06-29 19:36:26,570] [INFO] ===== Start GTDB Search =====
[2023-06-29 19:36:26,571] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023708705.1_ASM2370870v1_genomic.fna/markers.fasta)
[2023-06-29 19:36:26,571] [INFO] Task started: Blastn
[2023-06-29 19:36:26,571] [INFO] Running command: blastn -query GCA_023708705.1_ASM2370870v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg896d06cb-720c-467c-ba9d-9fdc91458dd7/dqc_reference/reference_markers_gtdb.fasta -out GCA_023708705.1_ASM2370870v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:36:27,409] [INFO] Task succeeded: Blastn
[2023-06-29 19:36:27,413] [INFO] Selected 12 target genomes.
[2023-06-29 19:36:27,413] [INFO] Target genome list was writen to GCA_023708705.1_ASM2370870v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 19:36:27,415] [INFO] Task started: fastANI
[2023-06-29 19:36:27,415] [INFO] Running command: fastANI --query /var/lib/cwl/stgf148b16a-3801-45f4-a977-160e62e69d4d/GCA_023708705.1_ASM2370870v1_genomic.fna.gz --refList GCA_023708705.1_ASM2370870v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023708705.1_ASM2370870v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 19:36:33,562] [INFO] Task succeeded: fastANI
[2023-06-29 19:36:33,576] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 19:36:33,576] [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_008681155.1	s__UBA1417 sp003531055	98.7126	815	1014	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1417	95.0	97.97	97.38	0.92	0.84	13	conclusive
GCA_004555625.1	s__UBA1417 sp004555625	80.1652	354	1014	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1417	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552925.1	s__UBA1417 sp900552925	80.0037	237	1014	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1417	95.0	98.06	97.73	0.91	0.83	5	-
GCA_900549945.1	s__UBA1417 sp900549945	79.7464	274	1014	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1417	95.0	98.46	97.65	0.85	0.74	4	-
GCA_017407665.1	s__UBA1417 sp017407665	78.9802	230	1014	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1417	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002305575.1	s__UBA1417 sp002305575	78.6166	306	1014	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1417	95.0	98.68	98.68	0.86	0.86	2	-
GCA_017623855.1	s__UBA1417 sp017623855	77.9894	175	1014	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1417	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018712435.1	s__Caccousia avicola	77.2731	81	1014	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Caccousia	95.0	98.29	98.29	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-06-29 19:36:33,579] [INFO] GTDB search result was written to GCA_023708705.1_ASM2370870v1_genomic.fna/result_gtdb.tsv
[2023-06-29 19:36:33,579] [INFO] ===== GTDB Search completed =====
[2023-06-29 19:36:33,583] [INFO] DFAST_QC result json was written to GCA_023708705.1_ASM2370870v1_genomic.fna/dqc_result.json
[2023-06-29 19:36:33,583] [INFO] DFAST_QC completed!
[2023-06-29 19:36:33,584] [INFO] Total running time: 0h1m4s