[2023-06-13 09:48:58,306] [INFO] DFAST_QC pipeline started.
[2023-06-13 09:48:58,308] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 09:48:58,308] [INFO] DQC Reference Directory: /var/lib/cwl/stgb77153a2-9eab-4222-a67a-2abcb60f5ae5/dqc_reference
[2023-06-13 09:48:59,519] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 09:48:59,520] [INFO] Task started: Prodigal
[2023-06-13 09:48:59,520] [INFO] Running command: gunzip -c /var/lib/cwl/stgb9fc5262-cdbb-441d-8b68-595359867740/GCA_947063495.1_SRR12358629_bin.24_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947063495.1_SRR12358629_bin.24_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947063495.1_SRR12358629_bin.24_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 09:49:09,810] [INFO] Task succeeded: Prodigal
[2023-06-13 09:49:09,810] [INFO] Task started: HMMsearch
[2023-06-13 09:49:09,811] [INFO] Running command: hmmsearch --tblout GCA_947063495.1_SRR12358629_bin.24_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb77153a2-9eab-4222-a67a-2abcb60f5ae5/dqc_reference/reference_markers.hmm GCA_947063495.1_SRR12358629_bin.24_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 09:49:10,097] [INFO] Task succeeded: HMMsearch
[2023-06-13 09:49:10,100] [INFO] Found 6/6 markers.
[2023-06-13 09:49:10,142] [INFO] Query marker FASTA was written to GCA_947063495.1_SRR12358629_bin.24_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-13 09:49:10,142] [INFO] Task started: Blastn
[2023-06-13 09:49:10,142] [INFO] Running command: blastn -query GCA_947063495.1_SRR12358629_bin.24_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb77153a2-9eab-4222-a67a-2abcb60f5ae5/dqc_reference/reference_markers.fasta -out GCA_947063495.1_SRR12358629_bin.24_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 09:49:10,784] [INFO] Task succeeded: Blastn
[2023-06-13 09:49:10,790] [INFO] Selected 26 target genomes.
[2023-06-13 09:49:10,790] [INFO] Target genome list was writen to GCA_947063495.1_SRR12358629_bin.24_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-13 09:49:10,793] [INFO] Task started: fastANI
[2023-06-13 09:49:10,793] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9fc5262-cdbb-441d-8b68-595359867740/GCA_947063495.1_SRR12358629_bin.24_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947063495.1_SRR12358629_bin.24_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947063495.1_SRR12358629_bin.24_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 09:49:27,150] [INFO] Task succeeded: fastANI
[2023-06-13 09:49:27,151] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb77153a2-9eab-4222-a67a-2abcb60f5ae5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 09:49:27,151] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb77153a2-9eab-4222-a67a-2abcb60f5ae5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 09:49:27,166] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 09:49:27,166] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 09:49:27,166] [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
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	76.9421	172	1322	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	76.8558	175	1322	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002959675.1	208479	208479	type	True	76.6697	127	1322	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_000160095.1	154046	154046	suspected-type	True	76.6667	91	1322	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_000154365.1	208479	208479	type	True	76.6545	127	1322	95	below_threshold
Enterocloster bolteae	strain=ATCC BAA-613	GCA_002234575.2	208479	208479	type	True	76.6375	129	1322	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	76.6265	102	1322	95	below_threshold
Hungatella effluvii	strain=DSM 24995	GCA_003201875.1	1096246	1096246	type	True	76.5094	102	1322	95	below_threshold
Massilistercora timonensis	strain=Marseille-P3756	GCA_900312975.1	2086584	2086584	type	True	76.3045	57	1322	95	below_threshold
Clostridium fessum	strain=SNUG30386	GCA_003024715.1	2126740	2126740	type	True	76.291	58	1322	95	below_threshold
Lacrimispora sphenoides	strain=ATCC 19403	GCA_900105615.1	29370	29370	type	True	76.1381	93	1322	95	below_threshold
Lacrimispora aerotolerans	strain=DSM 5434	GCA_000687555.1	36832	36832	type	True	76.1141	55	1322	95	below_threshold
Lacrimispora sphenoides	strain=NCTC507	GCA_900461315.1	29370	29370	type	True	76.0789	94	1322	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	75.5859	53	1322	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 09:49:27,168] [INFO] DFAST Taxonomy check result was written to GCA_947063495.1_SRR12358629_bin.24_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-13 09:49:27,169] [INFO] ===== Taxonomy check completed =====
[2023-06-13 09:49:27,169] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 09:49:27,169] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb77153a2-9eab-4222-a67a-2abcb60f5ae5/dqc_reference/checkm_data
[2023-06-13 09:49:27,171] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 09:49:27,216] [INFO] Task started: CheckM
[2023-06-13 09:49:27,216] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947063495.1_SRR12358629_bin.24_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947063495.1_SRR12358629_bin.24_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947063495.1_SRR12358629_bin.24_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-13 09:50:02,180] [INFO] Task succeeded: CheckM
[2023-06-13 09:50:02,183] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 09:50:02,203] [INFO] ===== Completeness check finished =====
[2023-06-13 09:50:02,203] [INFO] ===== Start GTDB Search =====
[2023-06-13 09:50:02,204] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947063495.1_SRR12358629_bin.24_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-13 09:50:02,204] [INFO] Task started: Blastn
[2023-06-13 09:50:02,204] [INFO] Running command: blastn -query GCA_947063495.1_SRR12358629_bin.24_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb77153a2-9eab-4222-a67a-2abcb60f5ae5/dqc_reference/reference_markers_gtdb.fasta -out GCA_947063495.1_SRR12358629_bin.24_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 09:50:03,254] [INFO] Task succeeded: Blastn
[2023-06-13 09:50:03,260] [INFO] Selected 12 target genomes.
[2023-06-13 09:50:03,260] [INFO] Target genome list was writen to GCA_947063495.1_SRR12358629_bin.24_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 09:50:03,261] [INFO] Task started: fastANI
[2023-06-13 09:50:03,262] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9fc5262-cdbb-441d-8b68-595359867740/GCA_947063495.1_SRR12358629_bin.24_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947063495.1_SRR12358629_bin.24_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947063495.1_SRR12358629_bin.24_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 09:50:12,950] [INFO] Task succeeded: fastANI
[2023-06-13 09:50:12,968] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 09:50:12,968] [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_910588865.1	s__UBA3402 sp910588865	98.8749	1100	1322	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3402	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_910577935.1	s__UBA3402 sp910577935	80.7209	597	1322	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3402	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910586845.1	s__UBA3402 sp910586845	79.785	525	1322	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3402	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585645.1	s__UBA3402 sp910585645	79.1328	452	1322	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3402	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588505.1	s__UBA3402 sp910588505	78.7671	395	1322	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3402	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910574345.1	s__UBA3402 sp910574345	78.7482	446	1322	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3402	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910575585.1	s__UBA3402 sp910575585	78.6741	458	1322	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3402	95.0	99.89	99.85	0.96	0.96	3	-
GCA_019114845.1	s__Lachnoclostridium_A stercoripullorum	77.3908	165	1322	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_A	95.0	98.44	98.44	0.80	0.80	2	-
GCA_910577765.1	s__Ventrimonas sp910577765	77.2194	199	1322	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910575795.1	s__Clostridium_Q sp910575795	76.7802	120	1322	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	99.66	99.05	0.95	0.91	4	-
GCF_002234575.2	s__Enterocloster bolteae	76.6549	128	1322	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.46	96.97	0.88	0.78	35	-
GCA_000155435.1	s__Enterocloster sp000155435	76.4208	131	1322	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	99.08	98.70	0.90	0.83	5	-
--------------------------------------------------------------------------------
[2023-06-13 09:50:12,970] [INFO] GTDB search result was written to GCA_947063495.1_SRR12358629_bin.24_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 09:50:12,970] [INFO] ===== GTDB Search completed =====
[2023-06-13 09:50:12,974] [INFO] DFAST_QC result json was written to GCA_947063495.1_SRR12358629_bin.24_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-13 09:50:12,974] [INFO] DFAST_QC completed!
[2023-06-13 09:50:12,975] [INFO] Total running time: 0h1m15s