[2024-01-24 12:07:06,586] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:07:06,588] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:07:06,588] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe5a8aef-1921-41b3-9a74-69fd1b8ff33c/dqc_reference
[2024-01-24 12:07:07,828] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:07:07,829] [INFO] Task started: Prodigal
[2024-01-24 12:07:07,829] [INFO] Running command: gunzip -c /var/lib/cwl/stg37814c1a-2318-451d-9514-6a66ba3e44bf/GCF_014288125.1_ASM1428812v1_genomic.fna.gz | prodigal -d GCF_014288125.1_ASM1428812v1_genomic.fna/cds.fna -a GCF_014288125.1_ASM1428812v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:17,056] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:17,057] [INFO] Task started: HMMsearch
[2024-01-24 12:07:17,057] [INFO] Running command: hmmsearch --tblout GCF_014288125.1_ASM1428812v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe5a8aef-1921-41b3-9a74-69fd1b8ff33c/dqc_reference/reference_markers.hmm GCF_014288125.1_ASM1428812v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:17,351] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:17,352] [INFO] Found 6/6 markers.
[2024-01-24 12:07:17,384] [INFO] Query marker FASTA was written to GCF_014288125.1_ASM1428812v1_genomic.fna/markers.fasta
[2024-01-24 12:07:17,385] [INFO] Task started: Blastn
[2024-01-24 12:07:17,385] [INFO] Running command: blastn -query GCF_014288125.1_ASM1428812v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe5a8aef-1921-41b3-9a74-69fd1b8ff33c/dqc_reference/reference_markers.fasta -out GCF_014288125.1_ASM1428812v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:17,996] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:18,000] [INFO] Selected 13 target genomes.
[2024-01-24 12:07:18,001] [INFO] Target genome list was writen to GCF_014288125.1_ASM1428812v1_genomic.fna/target_genomes.txt
[2024-01-24 12:07:18,004] [INFO] Task started: fastANI
[2024-01-24 12:07:18,005] [INFO] Running command: fastANI --query /var/lib/cwl/stg37814c1a-2318-451d-9514-6a66ba3e44bf/GCF_014288125.1_ASM1428812v1_genomic.fna.gz --refList GCF_014288125.1_ASM1428812v1_genomic.fna/target_genomes.txt --output GCF_014288125.1_ASM1428812v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:25,289] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:25,290] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe5a8aef-1921-41b3-9a74-69fd1b8ff33c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:25,291] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe5a8aef-1921-41b3-9a74-69fd1b8ff33c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:25,306] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:07:25,307] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:25,307] [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
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	98.3739	874	1004	95	conclusive
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	81.9735	450	1004	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	81.8969	420	1004	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	79.5094	290	1004	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	79.0071	263	1004	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	78.8389	271	1004	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	78.5518	220	1004	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	78.323	148	1004	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_003425665.1	2211183	2211183	type	True	78.2994	142	1004	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_008121455.1	2211183	2211183	type	True	78.2983	142	1004	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.8759	167	1004	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	76.4051	79	1004	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:25,309] [INFO] DFAST Taxonomy check result was written to GCF_014288125.1_ASM1428812v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:25,309] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:25,309] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:25,309] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe5a8aef-1921-41b3-9a74-69fd1b8ff33c/dqc_reference/checkm_data
[2024-01-24 12:07:25,311] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:25,341] [INFO] Task started: CheckM
[2024-01-24 12:07:25,341] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014288125.1_ASM1428812v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014288125.1_ASM1428812v1_genomic.fna/checkm_input GCF_014288125.1_ASM1428812v1_genomic.fna/checkm_result
[2024-01-24 12:07:56,745] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:56,747] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:56,782] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:56,783] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:56,783] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014288125.1_ASM1428812v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:56,784] [INFO] Task started: Blastn
[2024-01-24 12:07:56,784] [INFO] Running command: blastn -query GCF_014288125.1_ASM1428812v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe5a8aef-1921-41b3-9a74-69fd1b8ff33c/dqc_reference/reference_markers_gtdb.fasta -out GCF_014288125.1_ASM1428812v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:57,767] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:57,771] [INFO] Selected 14 target genomes.
[2024-01-24 12:07:57,771] [INFO] Target genome list was writen to GCF_014288125.1_ASM1428812v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:57,777] [INFO] Task started: fastANI
[2024-01-24 12:07:57,778] [INFO] Running command: fastANI --query /var/lib/cwl/stg37814c1a-2318-451d-9514-6a66ba3e44bf/GCF_014288125.1_ASM1428812v1_genomic.fna.gz --refList GCF_014288125.1_ASM1428812v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014288125.1_ASM1428812v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:07,083] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:07,095] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:07,096] [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_900199495.1	s__An92 sp900199495	98.799	876	1004	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	98.28	97.84	0.85	0.79	7	conclusive
GCA_018374635.1	s__An92 sp018374635	92.7519	685	1004	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002159175.1	s__An92 sp002159175	83.4311	556	1004	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	98.91	98.91	0.91	0.91	2	-
GCF_018917965.1	s__An92 sp018917965	82.3343	475	1004	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000239295.1	s__Flavonifractor plautii	81.8869	420	1004	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Flavonifractor	95.0	98.23	97.77	0.83	0.59	43	-
GCA_019118925.1	s__An92 sp019118925	81.7189	393	1004	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	99.98	99.98	0.93	0.93	2	-
GCA_019115265.1	s__An92 sp019115265	81.3795	375	1004	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__An92	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904419835.1	s__Pseudoflavonifractor sp904419835	80.5443	366	1004	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Pseudoflavonifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002160305.1	s__Lawsonibacter pullicola	80.5238	322	1004	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	98.22	97.83	0.90	0.75	8	-
GCF_900626145.1	s__Intestinimonas timonensis	80.4872	374	1004	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016899775.1	s__Lawsonibacter sp900545895	80.1118	321	1004	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	96.62	96.12	0.85	0.79	4	-
GCF_008727735.1	s__Lawsonibacter sp000177015	80.0542	300	1004	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	96.97	96.84	0.88	0.83	6	-
GCA_019115345.1	s__Intestinimonas stercorigallinarum	79.9086	260	1004	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019115785.1	s__Intestinimonas merdavium	79.2908	294	1004	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Intestinimonas	95.0	98.39	98.39	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:07,098] [INFO] GTDB search result was written to GCF_014288125.1_ASM1428812v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:07,098] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:07,102] [INFO] DFAST_QC result json was written to GCF_014288125.1_ASM1428812v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:07,102] [INFO] DFAST_QC completed!
[2024-01-24 12:08:07,102] [INFO] Total running time: 0h1m1s