[2023-06-07 21:33:36,342] [INFO] DFAST_QC pipeline started.
[2023-06-07 21:33:36,344] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 21:33:36,345] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0bae330-644c-4488-b9f7-37ee3546fcd0/dqc_reference
[2023-06-07 21:33:37,806] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 21:33:37,807] [INFO] Task started: Prodigal
[2023-06-07 21:33:37,807] [INFO] Running command: gunzip -c /var/lib/cwl/stga2a39766-4f0b-431a-88b1-4c8896467165/GCA_945868445.1_SRR17382103_bin.38_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945868445.1_SRR17382103_bin.38_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945868445.1_SRR17382103_bin.38_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 21:33:43,683] [INFO] Task succeeded: Prodigal
[2023-06-07 21:33:43,684] [INFO] Task started: HMMsearch
[2023-06-07 21:33:43,684] [INFO] Running command: hmmsearch --tblout GCA_945868445.1_SRR17382103_bin.38_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0bae330-644c-4488-b9f7-37ee3546fcd0/dqc_reference/reference_markers.hmm GCA_945868445.1_SRR17382103_bin.38_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-07 21:33:43,939] [INFO] Task succeeded: HMMsearch
[2023-06-07 21:33:43,941] [INFO] Found 6/6 markers.
[2023-06-07 21:33:43,971] [INFO] Query marker FASTA was written to GCA_945868445.1_SRR17382103_bin.38_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-07 21:33:43,971] [INFO] Task started: Blastn
[2023-06-07 21:33:43,973] [INFO] Running command: blastn -query GCA_945868445.1_SRR17382103_bin.38_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0bae330-644c-4488-b9f7-37ee3546fcd0/dqc_reference/reference_markers.fasta -out GCA_945868445.1_SRR17382103_bin.38_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 21:33:44,581] [INFO] Task succeeded: Blastn
[2023-06-07 21:33:44,585] [INFO] Selected 22 target genomes.
[2023-06-07 21:33:44,586] [INFO] Target genome list was writen to GCA_945868445.1_SRR17382103_bin.38_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-07 21:33:44,587] [INFO] Task started: fastANI
[2023-06-07 21:33:44,587] [INFO] Running command: fastANI --query /var/lib/cwl/stga2a39766-4f0b-431a-88b1-4c8896467165/GCA_945868445.1_SRR17382103_bin.38_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945868445.1_SRR17382103_bin.38_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945868445.1_SRR17382103_bin.38_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 21:33:55,720] [INFO] Task succeeded: fastANI
[2023-06-07 21:33:55,720] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0bae330-644c-4488-b9f7-37ee3546fcd0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 21:33:55,721] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0bae330-644c-4488-b9f7-37ee3546fcd0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 21:33:55,738] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 21:33:55,738] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 21:33:55,739] [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
Dorea longicatena	strain=DSM 13814	GCA_000154065.1	88431	88431	type	True	78.884	277	784	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	78.784	290	784	95	below_threshold
[Clostridium] scindens	strain=ATCC 35704	GCA_004295125.1	29347	29347	suspected-type	True	78.3768	202	784	95	below_threshold
[Clostridium] scindens	strain=ATCC 35704	GCA_000154505.1	29347	29347	suspected-type	True	78.3768	206	784	95	below_threshold
Dorea phocaeensis	strain=Marseille-P4003	GCA_900240315.1	2040291	2040291	type	True	78.1506	203	784	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_000169235.1	39486	39486	suspected-type	True	77.8121	180	784	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_025150245.1	39486	39486	suspected-type	True	77.7999	182	784	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	77.6194	133	784	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_009831375.1	33038	33038	suspected-type	True	77.6175	127	784	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	77.6022	130	784	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	77.5863	134	784	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	77.5793	132	784	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	77.5353	163	784	95	below_threshold
[Clostridium] hylemonae	strain=DSM 15053	GCA_000156515.1	89153	89153	type	True	77.3046	153	784	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	77.1904	118	784	95	below_threshold
Sporofaciens musculi	strain=WCA-9-b2	GCA_009830285.1	2681861	2681861	type	True	77.1864	125	784	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_000155205.1	46228	46228	type	True	77.1407	113	784	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	77.1216	115	784	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	76.4511	87	784	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 21:33:55,741] [INFO] DFAST Taxonomy check result was written to GCA_945868445.1_SRR17382103_bin.38_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-07 21:33:55,741] [INFO] ===== Taxonomy check completed =====
[2023-06-07 21:33:55,741] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 21:33:55,742] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0bae330-644c-4488-b9f7-37ee3546fcd0/dqc_reference/checkm_data
[2023-06-07 21:33:55,743] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 21:33:55,771] [INFO] Task started: CheckM
[2023-06-07 21:33:55,771] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945868445.1_SRR17382103_bin.38_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945868445.1_SRR17382103_bin.38_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945868445.1_SRR17382103_bin.38_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-07 21:34:20,625] [INFO] Task succeeded: CheckM
[2023-06-07 21:34:20,627] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.08%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 21:34:20,649] [INFO] ===== Completeness check finished =====
[2023-06-07 21:34:20,650] [INFO] ===== Start GTDB Search =====
[2023-06-07 21:34:20,650] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945868445.1_SRR17382103_bin.38_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-07 21:34:20,650] [INFO] Task started: Blastn
[2023-06-07 21:34:20,650] [INFO] Running command: blastn -query GCA_945868445.1_SRR17382103_bin.38_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0bae330-644c-4488-b9f7-37ee3546fcd0/dqc_reference/reference_markers_gtdb.fasta -out GCA_945868445.1_SRR17382103_bin.38_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 21:34:21,493] [INFO] Task succeeded: Blastn
[2023-06-07 21:34:21,498] [INFO] Selected 22 target genomes.
[2023-06-07 21:34:21,498] [INFO] Target genome list was writen to GCA_945868445.1_SRR17382103_bin.38_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 21:34:21,532] [INFO] Task started: fastANI
[2023-06-07 21:34:21,533] [INFO] Running command: fastANI --query /var/lib/cwl/stga2a39766-4f0b-431a-88b1-4c8896467165/GCA_945868445.1_SRR17382103_bin.38_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945868445.1_SRR17382103_bin.38_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945868445.1_SRR17382103_bin.38_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 21:34:33,633] [INFO] Task succeeded: fastANI
[2023-06-07 21:34:33,663] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 21:34:33,664] [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_016295505.1	s__Dorea_A sp016295505	98.9288	522	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000154065.1	s__Dorea_A longicatena	78.8904	276	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	98.55	97.61	0.85	0.69	49	-
GCA_900550865.1	s__Dorea_A sp900550865	78.6872	259	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001404875.1	s__Dorea_A longicatena_B	78.6497	277	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_A	95.0	97.75	96.72	0.80	0.69	20	-
GCF_003435815.1	s__CAG-317 sp000433215	78.3512	221	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-317	95.0	98.71	98.41	0.89	0.86	9	-
GCA_004560705.1	s__Bariatricus sp004560705	78.3161	157	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	99.19	99.19	0.81	0.81	2	-
GCF_900240315.1	s__Dorea_B phocaeensis	78.1687	202	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Dorea_B	95.0	98.22	97.28	0.87	0.81	8	-
GCA_900543415.1	s__CAG-317 sp900543415	77.9933	190	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-317	95.0	97.35	95.87	0.87	0.78	4	-
GCA_002492335.1	s__UBA7109 sp002492335	77.7139	113	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA7109	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013300725.1	s__Bariatricus comes_A	77.6903	163	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	98.85	98.85	0.86	0.86	2	-
GCA_000155875.1	s__Bariatricus comes	77.5483	153	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bariatricus	95.0	98.22	97.07	0.81	0.76	58	-
GCA_910575835.1	s__Sporofaciens sp910575835	77.512	155	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910574285.1	s__Sporofaciens sp009774295	77.3902	169	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	98.51	98.02	0.91	0.84	4	-
GCA_910574885.1	s__Sporofaciens sp910574885	77.2394	124	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	99.41	98.81	0.91	0.83	5	-
GCF_004345005.1	s__Extibacter muris	77.2248	136	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Extibacter	95.0	95.70	95.67	0.77	0.77	4	-
GCA_910585725.1	s__Sporofaciens sp910585725	77.1962	161	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584615.1	s__MD308 sp910584615	77.1735	136	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__MD308	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017566055.1	s__Extibacter sp017566055	77.1292	131	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Extibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544395.1	s__Ruminococcus_B sp900544395	76.9886	111	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ruminococcus_B	95.0	99.21	99.21	0.88	0.88	2	-
GCA_910587575.1	s__Sporofaciens sp910587575	76.8426	154	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002320245.1	s__Schaedlerella sp002320245	76.8066	103	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004556565.1	s__Schaedlerella sp004556565	76.3932	104	784	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Schaedlerella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-07 21:34:33,666] [INFO] GTDB search result was written to GCA_945868445.1_SRR17382103_bin.38_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-07 21:34:33,666] [INFO] ===== GTDB Search completed =====
[2023-06-07 21:34:33,671] [INFO] DFAST_QC result json was written to GCA_945868445.1_SRR17382103_bin.38_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-07 21:34:33,671] [INFO] DFAST_QC completed!
[2023-06-07 21:34:33,671] [INFO] Total running time: 0h0m57s