[2023-06-05 05:47:50,558] [INFO] DFAST_QC pipeline started.
[2023-06-05 05:47:50,561] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 05:47:50,562] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a2b43c2-5744-41ac-91ab-236621a4a052/dqc_reference
[2023-06-05 05:47:52,542] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 05:47:52,543] [INFO] Task started: Prodigal
[2023-06-05 05:47:52,544] [INFO] Running command: gunzip -c /var/lib/cwl/stg66cea5f4-3ab0-40ad-a0f8-9974e87b598c/GCA_934401975.1_ERR7738246_bin.32_genomic.fna.gz | prodigal -d GCA_934401975.1_ERR7738246_bin.32_genomic.fna/cds.fna -a GCA_934401975.1_ERR7738246_bin.32_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 05:48:00,416] [INFO] Task succeeded: Prodigal
[2023-06-05 05:48:00,416] [INFO] Task started: HMMsearch
[2023-06-05 05:48:00,417] [INFO] Running command: hmmsearch --tblout GCA_934401975.1_ERR7738246_bin.32_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a2b43c2-5744-41ac-91ab-236621a4a052/dqc_reference/reference_markers.hmm GCA_934401975.1_ERR7738246_bin.32_genomic.fna/protein.faa > /dev/null
[2023-06-05 05:48:00,686] [INFO] Task succeeded: HMMsearch
[2023-06-05 05:48:00,688] [INFO] Found 6/6 markers.
[2023-06-05 05:48:00,724] [INFO] Query marker FASTA was written to GCA_934401975.1_ERR7738246_bin.32_genomic.fna/markers.fasta
[2023-06-05 05:48:00,725] [INFO] Task started: Blastn
[2023-06-05 05:48:00,725] [INFO] Running command: blastn -query GCA_934401975.1_ERR7738246_bin.32_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a2b43c2-5744-41ac-91ab-236621a4a052/dqc_reference/reference_markers.fasta -out GCA_934401975.1_ERR7738246_bin.32_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 05:48:01,400] [INFO] Task succeeded: Blastn
[2023-06-05 05:48:01,404] [INFO] Selected 28 target genomes.
[2023-06-05 05:48:01,404] [INFO] Target genome list was writen to GCA_934401975.1_ERR7738246_bin.32_genomic.fna/target_genomes.txt
[2023-06-05 05:48:01,405] [INFO] Task started: fastANI
[2023-06-05 05:48:01,405] [INFO] Running command: fastANI --query /var/lib/cwl/stg66cea5f4-3ab0-40ad-a0f8-9974e87b598c/GCA_934401975.1_ERR7738246_bin.32_genomic.fna.gz --refList GCA_934401975.1_ERR7738246_bin.32_genomic.fna/target_genomes.txt --output GCA_934401975.1_ERR7738246_bin.32_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 05:48:17,232] [INFO] Task succeeded: fastANI
[2023-06-05 05:48:17,233] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a2b43c2-5744-41ac-91ab-236621a4a052/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 05:48:17,234] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a2b43c2-5744-41ac-91ab-236621a4a052/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 05:48:17,256] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 05:48:17,256] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 05:48:17,256] [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
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	79.5146	103	1035	95	below_threshold
Blautia intestinalis	strain=27-44	GCA_014297355.1	2763028	2763028	type	True	78.3918	172	1035	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	78.3262	144	1035	95	below_threshold
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	78.3111	176	1035	95	below_threshold
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	78.2376	170	1035	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	77.8983	158	1035	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	77.8851	201	1035	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_000153905.1	40520	40520	type	True	77.8326	157	1035	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	77.764	127	1035	95	below_threshold
Blautia producta	strain=DSM 2950	GCA_014131715.1	33035	33035	suspected-type	True	77.4886	129	1035	95	below_threshold
Blautia producta	strain=DSM 2950	GCA_000439125.1	33035	33035	suspected-type	True	77.4809	130	1035	95	below_threshold
Blautia producta	strain=ATCC 27340	GCA_000373885.1	33035	33035	suspected-type	True	77.4456	127	1035	95	below_threshold
Eubacterium ramulus	strain=ATCC 29099	GCA_000469345.1	39490	39490	type	True	77.4156	119	1035	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	77.2416	112	1035	95	below_threshold
Ruminococcus gauvreauii	strain=DSM 19829	GCA_000425525.1	438033	438033	type	True	77.2301	109	1035	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	77.2059	110	1035	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	77.2058	67	1035	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	77.1791	112	1035	95	below_threshold
Ruminococcus gauvreauii	strain=DSM 19829	GCA_025151995.1	438033	438033	type	True	77.1559	113	1035	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	77.1354	109	1035	95	below_threshold
Dorea phocaeensis	strain=Marseille-P4003	GCA_900240315.1	2040291	2040291	type	True	77.1288	61	1035	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_000160095.1	154046	154046	suspected-type	True	77.0847	62	1035	95	below_threshold
Blautia coccoides	strain=NCTC11035	GCA_900461125.1	1532	1532	type	True	76.9926	143	1035	95	below_threshold
Blautia coccoides	strain=DSM 935	GCA_004340925.1	1532	1532	type	True	76.9692	144	1035	95	below_threshold
Anaerobium acetethylicum	strain=GluBS11	GCA_900096945.1	1619234	1619234	type	True	76.5844	53	1035	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_000156535.1	166486	166486	type	True	76.4513	110	1035	95	below_threshold
Roseburia intestinalis	strain=L1 82	GCA_025151715.1	166486	166486	type	True	76.4283	113	1035	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_900537995.1	166486	166486	type	True	76.3941	115	1035	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 05:48:17,259] [INFO] DFAST Taxonomy check result was written to GCA_934401975.1_ERR7738246_bin.32_genomic.fna/tc_result.tsv
[2023-06-05 05:48:17,260] [INFO] ===== Taxonomy check completed =====
[2023-06-05 05:48:17,260] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 05:48:17,260] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a2b43c2-5744-41ac-91ab-236621a4a052/dqc_reference/checkm_data
[2023-06-05 05:48:17,261] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 05:48:17,296] [INFO] Task started: CheckM
[2023-06-05 05:48:17,297] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934401975.1_ERR7738246_bin.32_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934401975.1_ERR7738246_bin.32_genomic.fna/checkm_input GCA_934401975.1_ERR7738246_bin.32_genomic.fna/checkm_result
[2023-06-05 05:48:46,760] [INFO] Task succeeded: CheckM
[2023-06-05 05:48:46,762] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 05:48:46,783] [INFO] ===== Completeness check finished =====
[2023-06-05 05:48:46,784] [INFO] ===== Start GTDB Search =====
[2023-06-05 05:48:46,784] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934401975.1_ERR7738246_bin.32_genomic.fna/markers.fasta)
[2023-06-05 05:48:46,784] [INFO] Task started: Blastn
[2023-06-05 05:48:46,785] [INFO] Running command: blastn -query GCA_934401975.1_ERR7738246_bin.32_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a2b43c2-5744-41ac-91ab-236621a4a052/dqc_reference/reference_markers_gtdb.fasta -out GCA_934401975.1_ERR7738246_bin.32_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 05:48:47,920] [INFO] Task succeeded: Blastn
[2023-06-05 05:48:47,925] [INFO] Selected 12 target genomes.
[2023-06-05 05:48:47,925] [INFO] Target genome list was writen to GCA_934401975.1_ERR7738246_bin.32_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 05:48:47,928] [INFO] Task started: fastANI
[2023-06-05 05:48:47,928] [INFO] Running command: fastANI --query /var/lib/cwl/stg66cea5f4-3ab0-40ad-a0f8-9974e87b598c/GCA_934401975.1_ERR7738246_bin.32_genomic.fna.gz --refList GCA_934401975.1_ERR7738246_bin.32_genomic.fna/target_genomes_gtdb.txt --output GCA_934401975.1_ERR7738246_bin.32_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 05:48:55,817] [INFO] Task succeeded: fastANI
[2023-06-05 05:48:55,834] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 05:48:55,834] [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
GCF_004123145.1	s__Oliverpabstia faecicola	97.3724	923	1035	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oliverpabstia	95.0	97.72	97.58	0.88	0.80	5	conclusive
GCF_009696065.1	s__Oliverpabstia intestinalis	91.6176	780	1035	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oliverpabstia	95.0	97.25	96.88	0.81	0.78	19	-
GCA_002361775.1	s__Oliverpabstia sp002361775	79.5536	240	1035	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oliverpabstia	95.0	99.87	99.86	0.91	0.89	3	-
GCA_018374355.1	s__Oliverpabstia sp018374355	79.168	250	1035	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oliverpabstia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009929525.1	s__Oliverpabstia sp009929525	79.0527	239	1035	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oliverpabstia	95.0	99.76	99.76	0.92	0.92	2	-
GCA_004556655.1	s__Oliverpabstia sp004556655	78.9842	241	1035	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oliverpabstia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004562915.1	s__Oliverpabstia sp004562915	78.98	242	1035	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Oliverpabstia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902363685.1	s__UMGS1375 sp900066615	78.91	174	1035	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UMGS1375	95.0	98.15	97.87	0.85	0.79	16	-
GCA_018713585.1	s__Pullilachnospira stercoravium	77.5343	151	1035	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Pullilachnospira	95.0	97.91	97.84	0.85	0.79	6	-
GCA_905203555.1	s__Schaedlerella sp905203555	77.156	68	1035	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_900751785.1	s__Mediterraneibacter faecigallinarum	76.627	72	1035	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.56	97.84	0.86	0.78	4	-
GCA_016295505.1	s__Dorea_A sp016295505	76.5707	66	1035	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	-
--------------------------------------------------------------------------------
[2023-06-05 05:48:55,837] [INFO] GTDB search result was written to GCA_934401975.1_ERR7738246_bin.32_genomic.fna/result_gtdb.tsv
[2023-06-05 05:48:55,837] [INFO] ===== GTDB Search completed =====
[2023-06-05 05:48:55,842] [INFO] DFAST_QC result json was written to GCA_934401975.1_ERR7738246_bin.32_genomic.fna/dqc_result.json
[2023-06-05 05:48:55,842] [INFO] DFAST_QC completed!
[2023-06-05 05:48:55,842] [INFO] Total running time: 0h1m5s