[2023-06-28 22:38:01,487] [INFO] DFAST_QC pipeline started.
[2023-06-28 22:38:01,490] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 22:38:01,490] [INFO] DQC Reference Directory: /var/lib/cwl/stg148629e7-9abe-42a4-884d-7e47b3dab7c2/dqc_reference
[2023-06-28 22:38:02,681] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 22:38:02,682] [INFO] Task started: Prodigal
[2023-06-28 22:38:02,682] [INFO] Running command: gunzip -c /var/lib/cwl/stg7a086a6c-e1f7-485d-b513-82cb5a00c736/GCA_948439945.1_SRR17684615_bin.59_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_948439945.1_SRR17684615_bin.59_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_948439945.1_SRR17684615_bin.59_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 22:38:11,373] [INFO] Task succeeded: Prodigal
[2023-06-28 22:38:11,373] [INFO] Task started: HMMsearch
[2023-06-28 22:38:11,373] [INFO] Running command: hmmsearch --tblout GCA_948439945.1_SRR17684615_bin.59_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg148629e7-9abe-42a4-884d-7e47b3dab7c2/dqc_reference/reference_markers.hmm GCA_948439945.1_SRR17684615_bin.59_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 22:38:11,632] [INFO] Task succeeded: HMMsearch
[2023-06-28 22:38:11,634] [INFO] Found 6/6 markers.
[2023-06-28 22:38:11,665] [INFO] Query marker FASTA was written to GCA_948439945.1_SRR17684615_bin.59_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-28 22:38:11,666] [INFO] Task started: Blastn
[2023-06-28 22:38:11,666] [INFO] Running command: blastn -query GCA_948439945.1_SRR17684615_bin.59_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg148629e7-9abe-42a4-884d-7e47b3dab7c2/dqc_reference/reference_markers.fasta -out GCA_948439945.1_SRR17684615_bin.59_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 22:38:12,270] [INFO] Task succeeded: Blastn
[2023-06-28 22:38:12,275] [INFO] Selected 17 target genomes.
[2023-06-28 22:38:12,275] [INFO] Target genome list was writen to GCA_948439945.1_SRR17684615_bin.59_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-28 22:38:12,279] [INFO] Task started: fastANI
[2023-06-28 22:38:12,280] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a086a6c-e1f7-485d-b513-82cb5a00c736/GCA_948439945.1_SRR17684615_bin.59_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948439945.1_SRR17684615_bin.59_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_948439945.1_SRR17684615_bin.59_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 22:38:21,531] [INFO] Task succeeded: fastANI
[2023-06-28 22:38:21,532] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg148629e7-9abe-42a4-884d-7e47b3dab7c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 22:38:21,533] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg148629e7-9abe-42a4-884d-7e47b3dab7c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 22:38:21,555] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 22:38:21,555] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 22:38:21,555] [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
Schaedlerella arabinosiphila	strain=DSM 106076	GCA_003885045.1	2044587	2044587	type	True	85.6574	790	1134	95	below_threshold
Faecalicatena faecalis	strain=AGMB00832	GCA_012524165.2	2726362	2726362	type	True	77.1341	112	1134	95	below_threshold
Massilistercora timonensis	strain=Marseille-P3756	GCA_900312975.1	2086584	2086584	type	True	76.9221	104	1134	95	below_threshold
Mediterraneibacter massiliensis	strain=Marseille-P2086	GCA_001487105.1	1720300	1720300	type	True	76.6393	75	1134	95	below_threshold
[Ruminococcus] torques	strain=ATCC 27756	GCA_000153925.1	33039	33039	type	True	76.636	57	1134	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	76.5664	109	1134	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	76.5345	110	1134	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_009831375.1	33038	33038	suspected-type	True	76.5208	111	1134	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	76.4982	113	1134	95	below_threshold
Mediterraneibacter catenae	strain=SW178	GCA_008691045.1	2594882	2594882	type	True	76.4933	100	1134	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	76.4911	113	1134	95	below_threshold
[Clostridium] scindens	strain=ATCC 35704	GCA_000154505.1	29347	29347	suspected-type	True	76.473	74	1134	95	below_threshold
Muricomes intestini	strain=DSM 29489	GCA_004346165.1	1796634	1796634	type	True	76.4271	68	1134	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 22:38:21,557] [INFO] DFAST Taxonomy check result was written to GCA_948439945.1_SRR17684615_bin.59_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-28 22:38:21,558] [INFO] ===== Taxonomy check completed =====
[2023-06-28 22:38:21,558] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 22:38:21,558] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg148629e7-9abe-42a4-884d-7e47b3dab7c2/dqc_reference/checkm_data
[2023-06-28 22:38:21,559] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 22:38:21,599] [INFO] Task started: CheckM
[2023-06-28 22:38:21,600] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_948439945.1_SRR17684615_bin.59_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_948439945.1_SRR17684615_bin.59_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_948439945.1_SRR17684615_bin.59_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-28 22:38:52,675] [INFO] Task succeeded: CheckM
[2023-06-28 22:38:52,676] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 22:38:52,698] [INFO] ===== Completeness check finished =====
[2023-06-28 22:38:52,699] [INFO] ===== Start GTDB Search =====
[2023-06-28 22:38:52,699] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_948439945.1_SRR17684615_bin.59_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-28 22:38:52,699] [INFO] Task started: Blastn
[2023-06-28 22:38:52,699] [INFO] Running command: blastn -query GCA_948439945.1_SRR17684615_bin.59_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg148629e7-9abe-42a4-884d-7e47b3dab7c2/dqc_reference/reference_markers_gtdb.fasta -out GCA_948439945.1_SRR17684615_bin.59_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 22:38:53,541] [INFO] Task succeeded: Blastn
[2023-06-28 22:38:53,547] [INFO] Selected 6 target genomes.
[2023-06-28 22:38:53,547] [INFO] Target genome list was writen to GCA_948439945.1_SRR17684615_bin.59_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 22:38:53,552] [INFO] Task started: fastANI
[2023-06-28 22:38:53,552] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a086a6c-e1f7-485d-b513-82cb5a00c736/GCA_948439945.1_SRR17684615_bin.59_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948439945.1_SRR17684615_bin.59_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_948439945.1_SRR17684615_bin.59_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 22:39:01,989] [INFO] Task succeeded: fastANI
[2023-06-28 22:39:01,997] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 22:39:01,997] [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_000403295.2	s__Schaedlerella sp000403295	97.2057	948	1134	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	98.10	98.10	0.85	0.85	2	conclusive
GCA_910575475.1	s__Schaedlerella sp910575475	88.353	847	1134	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	99.35	99.35	0.93	0.93	2	-
GCA_009911175.1	s__Schaedlerella sp009911175	88.0427	799	1134	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	98.09	98.08	0.79	0.79	3	-
GCF_003885045.1	s__Schaedlerella arabinosiphila	85.6162	794	1134	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	97.52	96.80	0.74	0.68	10	-
GCA_009774255.1	s__Schaedlerella sp009774255	81.5569	566	1134	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 22:39:01,999] [INFO] GTDB search result was written to GCA_948439945.1_SRR17684615_bin.59_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 22:39:02,000] [INFO] ===== GTDB Search completed =====
[2023-06-28 22:39:02,003] [INFO] DFAST_QC result json was written to GCA_948439945.1_SRR17684615_bin.59_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-28 22:39:02,003] [INFO] DFAST_QC completed!
[2023-06-28 22:39:02,003] [INFO] Total running time: 0h1m1s