[2023-06-29 16:35:15,667] [INFO] DFAST_QC pipeline started.
[2023-06-29 16:35:15,669] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 16:35:15,669] [INFO] DQC Reference Directory: /var/lib/cwl/stg10b46498-d7ce-43cc-8f6a-233e7ad22f58/dqc_reference
[2023-06-29 16:35:16,914] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 16:35:16,915] [INFO] Task started: Prodigal
[2023-06-29 16:35:16,915] [INFO] Running command: gunzip -c /var/lib/cwl/stga479696c-24a1-4bec-a7d9-da6cb97da404/GCA_937898055.1_ERR318699_bin.54_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937898055.1_ERR318699_bin.54_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937898055.1_ERR318699_bin.54_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 16:35:23,550] [INFO] Task succeeded: Prodigal
[2023-06-29 16:35:23,550] [INFO] Task started: HMMsearch
[2023-06-29 16:35:23,551] [INFO] Running command: hmmsearch --tblout GCA_937898055.1_ERR318699_bin.54_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg10b46498-d7ce-43cc-8f6a-233e7ad22f58/dqc_reference/reference_markers.hmm GCA_937898055.1_ERR318699_bin.54_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 16:35:23,822] [INFO] Task succeeded: HMMsearch
[2023-06-29 16:35:23,824] [INFO] Found 6/6 markers.
[2023-06-29 16:35:23,853] [INFO] Query marker FASTA was written to GCA_937898055.1_ERR318699_bin.54_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 16:35:23,853] [INFO] Task started: Blastn
[2023-06-29 16:35:23,854] [INFO] Running command: blastn -query GCA_937898055.1_ERR318699_bin.54_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg10b46498-d7ce-43cc-8f6a-233e7ad22f58/dqc_reference/reference_markers.fasta -out GCA_937898055.1_ERR318699_bin.54_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:35:24,456] [INFO] Task succeeded: Blastn
[2023-06-29 16:35:24,461] [INFO] Selected 14 target genomes.
[2023-06-29 16:35:24,462] [INFO] Target genome list was writen to GCA_937898055.1_ERR318699_bin.54_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 16:35:24,467] [INFO] Task started: fastANI
[2023-06-29 16:35:24,467] [INFO] Running command: fastANI --query /var/lib/cwl/stga479696c-24a1-4bec-a7d9-da6cb97da404/GCA_937898055.1_ERR318699_bin.54_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937898055.1_ERR318699_bin.54_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937898055.1_ERR318699_bin.54_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 16:35:30,514] [INFO] Task succeeded: fastANI
[2023-06-29 16:35:30,515] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg10b46498-d7ce-43cc-8f6a-233e7ad22f58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 16:35:30,515] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg10b46498-d7ce-43cc-8f6a-233e7ad22f58/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 16:35:30,527] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 16:35:30,527] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 16:35:30,527] [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
Megasphaera elsdenii	strain=ATCC 25940	GCA_003010495.1	907	907	type	True	79.1526	290	830	95	below_threshold
Megasphaera elsdenii	strain=DSM 20460	GCA_000283495.2	907	907	type	True	79.1213	289	830	95	below_threshold
Megasphaera massiliensis	strain=NP3	GCA_000455225.1	1232428	1232428	suspected-type	True	77.7713	200	830	95	below_threshold
Megasphaera stantonii	strain=AJH120	GCA_003367905.1	2144175	2144175	type	True	77.6448	197	830	95	below_threshold
'Megasphaera vaginalis' Bordigoni et al. 2020	strain=Marseille-P4857	GCA_900240295.1	2045301	2045301	type	True	77.6159	121	830	95	below_threshold
Megasphaera stantonii	strain=AJH120	GCA_003030445.1	2144175	2144175	type	True	77.5963	195	830	95	below_threshold
Megasphaera cerevisiae	strain=DSM 20462	GCA_001045675.1	39029	39029	type	True	77.2096	117	830	95	below_threshold
Megasphaera cerevisiae	strain=DSM 20462	GCA_900167325.1	39029	39029	type	True	77.1865	115	830	95	below_threshold
Colibacter massiliensis	strain=Marseille-P2911	GCA_900095855.1	1852379	1852379	type	True	76.1883	64	830	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 16:35:30,529] [INFO] DFAST Taxonomy check result was written to GCA_937898055.1_ERR318699_bin.54_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 16:35:30,530] [INFO] ===== Taxonomy check completed =====
[2023-06-29 16:35:30,530] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 16:35:30,530] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg10b46498-d7ce-43cc-8f6a-233e7ad22f58/dqc_reference/checkm_data
[2023-06-29 16:35:30,531] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 16:35:30,559] [INFO] Task started: CheckM
[2023-06-29 16:35:30,560] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937898055.1_ERR318699_bin.54_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937898055.1_ERR318699_bin.54_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937898055.1_ERR318699_bin.54_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 16:35:56,752] [INFO] Task succeeded: CheckM
[2023-06-29 16:35:56,753] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.45%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 16:35:56,773] [INFO] ===== Completeness check finished =====
[2023-06-29 16:35:56,773] [INFO] ===== Start GTDB Search =====
[2023-06-29 16:35:56,774] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937898055.1_ERR318699_bin.54_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 16:35:56,774] [INFO] Task started: Blastn
[2023-06-29 16:35:56,774] [INFO] Running command: blastn -query GCA_937898055.1_ERR318699_bin.54_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg10b46498-d7ce-43cc-8f6a-233e7ad22f58/dqc_reference/reference_markers_gtdb.fasta -out GCA_937898055.1_ERR318699_bin.54_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 16:35:57,658] [INFO] Task succeeded: Blastn
[2023-06-29 16:35:57,663] [INFO] Selected 12 target genomes.
[2023-06-29 16:35:57,663] [INFO] Target genome list was writen to GCA_937898055.1_ERR318699_bin.54_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 16:35:57,671] [INFO] Task started: fastANI
[2023-06-29 16:35:57,671] [INFO] Running command: fastANI --query /var/lib/cwl/stga479696c-24a1-4bec-a7d9-da6cb97da404/GCA_937898055.1_ERR318699_bin.54_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937898055.1_ERR318699_bin.54_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937898055.1_ERR318699_bin.54_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 16:36:03,058] [INFO] Task succeeded: fastANI
[2023-06-29 16:36:03,077] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 16:36:03,077] [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_900095875.1	s__Caecibacter massiliensis	98.7092	765	830	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Caecibacter	95.0	98.76	97.64	0.92	0.86	18	conclusive
GCF_003467125.1	s__Caecibacter sp003467125	88.5912	720	830	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Caecibacter	95.0	98.80	97.67	0.92	0.89	5	-
GCF_014269395.1	s__Caecibacter hominis	79.3316	311	830	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Caecibacter	95.0	99.84	99.81	0.96	0.95	4	-
GCA_902388315.1	s__Megasphaera sp902388315	79.228	236	830	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.43	99.12	0.87	0.82	3	-
GCF_003010495.1	s__Megasphaera elsdenii	79.1207	292	830	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	98.27	97.55	0.90	0.81	29	-
GCF_000417505.1	s__Megasphaera sp000417505	79.0144	275	830	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.18	97.65	0.90	0.81	11	-
GCA_900548635.1	s__Megasphaera sp900548635	78.8209	208	830	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.28	98.56	0.89	0.79	3	-
GCA_002319965.1	s__Megasphaera sp002319965	77.8552	157	830	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	98.41	98.03	0.89	0.89	4	-
GCF_000455225.1	s__Megasphaera massiliensis	77.8047	198	830	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	98.41	96.06	0.94	0.88	8	-
GCF_900240295.1	s__Anaeroglobus vaginalis	77.6159	121	830	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Anaeroglobus	95.0	99.10	99.10	0.91	0.91	2	-
GCA_002431345.1	s__Megasphaera sp002431345	77.4635	156	830	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.44	99.22	0.90	0.87	5	-
GCF_900095855.1	s__Anaeroglobus massiliensis	76.1883	64	830	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Anaeroglobus	95.0	99.40	98.79	0.98	0.97	3	-
--------------------------------------------------------------------------------
[2023-06-29 16:36:03,079] [INFO] GTDB search result was written to GCA_937898055.1_ERR318699_bin.54_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 16:36:03,080] [INFO] ===== GTDB Search completed =====
[2023-06-29 16:36:03,085] [INFO] DFAST_QC result json was written to GCA_937898055.1_ERR318699_bin.54_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 16:36:03,085] [INFO] DFAST_QC completed!
[2023-06-29 16:36:03,085] [INFO] Total running time: 0h0m47s