[2023-06-19 12:32:46,155] [INFO] DFAST_QC pipeline started.
[2023-06-19 12:32:46,158] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 12:32:46,158] [INFO] DQC Reference Directory: /var/lib/cwl/stgadd7683d-94a1-4bc3-897d-db55a598bcfb/dqc_reference
[2023-06-19 12:32:49,595] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 12:32:49,597] [INFO] Task started: Prodigal
[2023-06-19 12:32:49,597] [INFO] Running command: gunzip -c /var/lib/cwl/stg425a8bb4-3ba7-4876-8724-d5a1f9b67de0/GCA_937906845.1_DRR014734_bin.25_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937906845.1_DRR014734_bin.25_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937906845.1_DRR014734_bin.25_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 12:33:02,461] [INFO] Task succeeded: Prodigal
[2023-06-19 12:33:02,462] [INFO] Task started: HMMsearch
[2023-06-19 12:33:02,462] [INFO] Running command: hmmsearch --tblout GCA_937906845.1_DRR014734_bin.25_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgadd7683d-94a1-4bc3-897d-db55a598bcfb/dqc_reference/reference_markers.hmm GCA_937906845.1_DRR014734_bin.25_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-19 12:33:02,779] [INFO] Task succeeded: HMMsearch
[2023-06-19 12:33:02,780] [INFO] Found 6/6 markers.
[2023-06-19 12:33:02,838] [INFO] Query marker FASTA was written to GCA_937906845.1_DRR014734_bin.25_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-19 12:33:02,839] [INFO] Task started: Blastn
[2023-06-19 12:33:02,839] [INFO] Running command: blastn -query GCA_937906845.1_DRR014734_bin.25_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgadd7683d-94a1-4bc3-897d-db55a598bcfb/dqc_reference/reference_markers.fasta -out GCA_937906845.1_DRR014734_bin.25_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 12:33:03,525] [INFO] Task succeeded: Blastn
[2023-06-19 12:33:03,530] [INFO] Selected 29 target genomes.
[2023-06-19 12:33:03,530] [INFO] Target genome list was writen to GCA_937906845.1_DRR014734_bin.25_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-19 12:33:03,537] [INFO] Task started: fastANI
[2023-06-19 12:33:03,538] [INFO] Running command: fastANI --query /var/lib/cwl/stg425a8bb4-3ba7-4876-8724-d5a1f9b67de0/GCA_937906845.1_DRR014734_bin.25_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937906845.1_DRR014734_bin.25_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937906845.1_DRR014734_bin.25_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 12:33:24,819] [INFO] Task succeeded: fastANI
[2023-06-19 12:33:24,820] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgadd7683d-94a1-4bc3-897d-db55a598bcfb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 12:33:24,820] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgadd7683d-94a1-4bc3-897d-db55a598bcfb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 12:33:24,834] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 12:33:24,834] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 12:33:24,834] [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
Massilistercora timonensis	strain=Marseille-P3756	GCA_900312975.1	2086584	2086584	type	True	77.2296	71	1510	95	below_threshold
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	76.6387	109	1510	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	76.5383	88	1510	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	76.4698	90	1510	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	76.2418	117	1510	95	below_threshold
Wansuia hejianensis	strain=NSJ-29	GCA_014337215.1	2763667	2763667	type	True	76.0423	52	1510	95	below_threshold
Diplocloster modestus	strain=ASD4241	GCA_019042245.1	2850322	2850322	type	True	75.7504	50	1510	95	below_threshold
Diplocloster agilis	strain=ASD5720	GCA_019042275.1	2850323	2850323	type	True	75.7386	53	1510	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_002221555.2	1796616	1796616	type	True	75.6619	53	1510	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_001689125.2	1796616	1796616	type	True	75.6432	54	1510	95	below_threshold
Blautia pseudococcoides	strain=YL58	GCA_016696745.1	1796616	1796616	type	True	75.6432	54	1510	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 12:33:24,837] [INFO] DFAST Taxonomy check result was written to GCA_937906845.1_DRR014734_bin.25_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-19 12:33:24,837] [INFO] ===== Taxonomy check completed =====
[2023-06-19 12:33:24,837] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 12:33:24,838] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgadd7683d-94a1-4bc3-897d-db55a598bcfb/dqc_reference/checkm_data
[2023-06-19 12:33:24,839] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 12:33:24,895] [INFO] Task started: CheckM
[2023-06-19 12:33:24,895] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937906845.1_DRR014734_bin.25_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937906845.1_DRR014734_bin.25_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937906845.1_DRR014734_bin.25_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-19 12:34:05,363] [INFO] Task succeeded: CheckM
[2023-06-19 12:34:05,364] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 12:34:05,391] [INFO] ===== Completeness check finished =====
[2023-06-19 12:34:05,391] [INFO] ===== Start GTDB Search =====
[2023-06-19 12:34:05,392] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937906845.1_DRR014734_bin.25_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-19 12:34:05,392] [INFO] Task started: Blastn
[2023-06-19 12:34:05,392] [INFO] Running command: blastn -query GCA_937906845.1_DRR014734_bin.25_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgadd7683d-94a1-4bc3-897d-db55a598bcfb/dqc_reference/reference_markers_gtdb.fasta -out GCA_937906845.1_DRR014734_bin.25_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 12:34:06,477] [INFO] Task succeeded: Blastn
[2023-06-19 12:34:06,482] [INFO] Selected 6 target genomes.
[2023-06-19 12:34:06,483] [INFO] Target genome list was writen to GCA_937906845.1_DRR014734_bin.25_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 12:34:06,512] [INFO] Task started: fastANI
[2023-06-19 12:34:06,512] [INFO] Running command: fastANI --query /var/lib/cwl/stg425a8bb4-3ba7-4876-8724-d5a1f9b67de0/GCA_937906845.1_DRR014734_bin.25_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937906845.1_DRR014734_bin.25_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937906845.1_DRR014734_bin.25_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 12:34:12,765] [INFO] Task succeeded: fastANI
[2023-06-19 12:34:12,771] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 12:34:12,772] [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_910585015.1	s__Acetatifactor sp910585015	98.7165	1162	1510	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_910583845.1	s__Acetatifactor sp910583845	82.3007	872	1510	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011959105.1	s__Acetatifactor sp011959105	81.6515	723	1510	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	99.00	99.00	0.85	0.85	2	-
GCA_014804645.1	s__Acetatifactor sp014804645	81.2839	736	1510	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577235.1	s__Acetatifactor sp910577235	81.0337	726	1510	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584375.1	s__Acetatifactor sp910584375	80.6608	706	1510	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 12:34:12,773] [INFO] GTDB search result was written to GCA_937906845.1_DRR014734_bin.25_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-19 12:34:12,774] [INFO] ===== GTDB Search completed =====
[2023-06-19 12:34:12,777] [INFO] DFAST_QC result json was written to GCA_937906845.1_DRR014734_bin.25_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-19 12:34:12,777] [INFO] DFAST_QC completed!
[2023-06-19 12:34:12,777] [INFO] Total running time: 0h1m27s