[2023-06-28 18:40:41,684] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:40:41,697] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:40:41,697] [INFO] DQC Reference Directory: /var/lib/cwl/stg9bc0af14-54ac-42dc-8c3c-6f54a08ace21/dqc_reference
[2023-06-28 18:40:44,128] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:40:44,129] [INFO] Task started: Prodigal
[2023-06-28 18:40:44,129] [INFO] Running command: gunzip -c /var/lib/cwl/stgfcdae542-4e9f-4ccd-9218-c77acdb2305a/GCA_944385965.1_E14_bin8_genomic.fna.gz | prodigal -d GCA_944385965.1_E14_bin8_genomic.fna/cds.fna -a GCA_944385965.1_E14_bin8_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:40:50,416] [INFO] Task succeeded: Prodigal
[2023-06-28 18:40:50,417] [INFO] Task started: HMMsearch
[2023-06-28 18:40:50,417] [INFO] Running command: hmmsearch --tblout GCA_944385965.1_E14_bin8_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9bc0af14-54ac-42dc-8c3c-6f54a08ace21/dqc_reference/reference_markers.hmm GCA_944385965.1_E14_bin8_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:40:50,662] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:40:50,664] [INFO] Found 6/6 markers.
[2023-06-28 18:40:50,690] [INFO] Query marker FASTA was written to GCA_944385965.1_E14_bin8_genomic.fna/markers.fasta
[2023-06-28 18:40:50,691] [INFO] Task started: Blastn
[2023-06-28 18:40:50,691] [INFO] Running command: blastn -query GCA_944385965.1_E14_bin8_genomic.fna/markers.fasta -db /var/lib/cwl/stg9bc0af14-54ac-42dc-8c3c-6f54a08ace21/dqc_reference/reference_markers.fasta -out GCA_944385965.1_E14_bin8_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:40:51,324] [INFO] Task succeeded: Blastn
[2023-06-28 18:40:51,329] [INFO] Selected 20 target genomes.
[2023-06-28 18:40:51,329] [INFO] Target genome list was writen to GCA_944385965.1_E14_bin8_genomic.fna/target_genomes.txt
[2023-06-28 18:40:51,332] [INFO] Task started: fastANI
[2023-06-28 18:40:51,332] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcdae542-4e9f-4ccd-9218-c77acdb2305a/GCA_944385965.1_E14_bin8_genomic.fna.gz --refList GCA_944385965.1_E14_bin8_genomic.fna/target_genomes.txt --output GCA_944385965.1_E14_bin8_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:41:02,666] [INFO] Task succeeded: fastANI
[2023-06-28 18:41:02,666] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9bc0af14-54ac-42dc-8c3c-6f54a08ace21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:41:02,667] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9bc0af14-54ac-42dc-8c3c-6f54a08ace21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:41:02,675] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 18:41:02,675] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 18:41:02,676] [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
Angelakisella massiliensis	strain=Marseille-P3217	GCA_900104675.1	1871018	1871018	type	True	77.7942	76	743	95	below_threshold
Anaerotruncus rubiinfantis	strain=MT15	GCA_900078395.1	1720200	1720200	type	True	77.4678	57	743	95	below_threshold
Anaerotruncus massiliensis	strain=AT3	GCA_900199635.1	1673720	1673720	type	True	76.8891	68	743	95	below_threshold
Anaerotruncus colihominis	strain=DSM 17241	GCA_000154565.1	169435	169435	type	True	76.7557	51	743	95	below_threshold
Phocea massiliensis	strain=Marseille-P2769	GCA_900104615.1	1841867	1841867	type	True	76.632	52	743	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 18:41:02,680] [INFO] DFAST Taxonomy check result was written to GCA_944385965.1_E14_bin8_genomic.fna/tc_result.tsv
[2023-06-28 18:41:02,680] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:41:02,681] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:41:02,681] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9bc0af14-54ac-42dc-8c3c-6f54a08ace21/dqc_reference/checkm_data
[2023-06-28 18:41:02,682] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:41:02,709] [INFO] Task started: CheckM
[2023-06-28 18:41:02,709] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944385965.1_E14_bin8_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944385965.1_E14_bin8_genomic.fna/checkm_input GCA_944385965.1_E14_bin8_genomic.fna/checkm_result
[2023-06-28 18:41:27,610] [INFO] Task succeeded: CheckM
[2023-06-28 18:41:27,612] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 18:41:27,636] [INFO] ===== Completeness check finished =====
[2023-06-28 18:41:27,637] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:41:27,637] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944385965.1_E14_bin8_genomic.fna/markers.fasta)
[2023-06-28 18:41:27,638] [INFO] Task started: Blastn
[2023-06-28 18:41:27,638] [INFO] Running command: blastn -query GCA_944385965.1_E14_bin8_genomic.fna/markers.fasta -db /var/lib/cwl/stg9bc0af14-54ac-42dc-8c3c-6f54a08ace21/dqc_reference/reference_markers_gtdb.fasta -out GCA_944385965.1_E14_bin8_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:41:28,682] [INFO] Task succeeded: Blastn
[2023-06-28 18:41:28,688] [INFO] Selected 24 target genomes.
[2023-06-28 18:41:28,688] [INFO] Target genome list was writen to GCA_944385965.1_E14_bin8_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:41:28,704] [INFO] Task started: fastANI
[2023-06-28 18:41:28,704] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcdae542-4e9f-4ccd-9218-c77acdb2305a/GCA_944385965.1_E14_bin8_genomic.fna.gz --refList GCA_944385965.1_E14_bin8_genomic.fna/target_genomes_gtdb.txt --output GCA_944385965.1_E14_bin8_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:41:37,700] [INFO] Task succeeded: fastANI
[2023-06-28 18:41:37,714] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 18:41:37,714] [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_900104675.1	s__Angelakisella massiliensis	77.7183	77	743	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Angelakisella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000403395.2	s__Anaerotruncus sp000403395	77.5055	66	743	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	98.44	98.36	0.83	0.79	7	-
GCA_910586875.1	s__Anaerotruncus sp910586875	77.4956	100	743	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078395.1	s__Anaerotruncus rubiinfantis	77.4678	57	743	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	99.23	99.21	0.89	0.86	5	-
GCF_900199635.1	s__Anaerotruncus massiliensis	76.8891	68	743	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	98.56	98.01	0.95	0.93	6	-
GCA_019114825.1	s__Anaerotruncus excrementipullorum	76.8293	86	743	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	99.88	99.88	0.94	0.94	2	-
GCF_000154565.1	s__Anaerotruncus colihominis	76.7557	51	743	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	98.95	97.75	0.87	0.80	16	-
GCF_010206195.1	s__Anaerotruncus colihominis_A	76.7007	52	743	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	98.98	98.75	0.89	0.87	3	-
GCF_904387055.1	s__Heteroruminococcus faecigallinarum	76.639	50	743	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Heteroruminococcus	95.0	99.97	99.97	0.96	0.96	2	-
GCF_900104615.1	s__Phocea massiliensis	76.632	52	743	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Phocea	95.0	99.45	98.96	0.93	0.87	5	-
GCA_904398655.1	s__Anaerotruncus sp904398655	76.2478	64	743	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Anaerotruncus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 18:41:37,716] [INFO] GTDB search result was written to GCA_944385965.1_E14_bin8_genomic.fna/result_gtdb.tsv
[2023-06-28 18:41:37,717] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:41:37,720] [INFO] DFAST_QC result json was written to GCA_944385965.1_E14_bin8_genomic.fna/dqc_result.json
[2023-06-28 18:41:37,720] [INFO] DFAST_QC completed!
[2023-06-28 18:41:37,720] [INFO] Total running time: 0h0m56s