[2023-06-17 09:02:40,246] [INFO] DFAST_QC pipeline started.
[2023-06-17 09:02:40,249] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 09:02:40,249] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c0d1aa7-57fa-4e97-9125-42a28bc96776/dqc_reference
[2023-06-17 09:02:41,471] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 09:02:41,472] [INFO] Task started: Prodigal
[2023-06-17 09:02:41,472] [INFO] Running command: gunzip -c /var/lib/cwl/stg537c468b-6ab9-4536-91f3-0d8e99d39f36/GCA_009379975.1_ASM937997v1_genomic.fna.gz | prodigal -d GCA_009379975.1_ASM937997v1_genomic.fna/cds.fna -a GCA_009379975.1_ASM937997v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 09:02:54,024] [INFO] Task succeeded: Prodigal
[2023-06-17 09:02:54,025] [INFO] Task started: HMMsearch
[2023-06-17 09:02:54,025] [INFO] Running command: hmmsearch --tblout GCA_009379975.1_ASM937997v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c0d1aa7-57fa-4e97-9125-42a28bc96776/dqc_reference/reference_markers.hmm GCA_009379975.1_ASM937997v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 09:02:54,285] [INFO] Task succeeded: HMMsearch
[2023-06-17 09:02:54,287] [INFO] Found 6/6 markers.
[2023-06-17 09:02:54,326] [INFO] Query marker FASTA was written to GCA_009379975.1_ASM937997v1_genomic.fna/markers.fasta
[2023-06-17 09:02:54,326] [INFO] Task started: Blastn
[2023-06-17 09:02:54,326] [INFO] Running command: blastn -query GCA_009379975.1_ASM937997v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c0d1aa7-57fa-4e97-9125-42a28bc96776/dqc_reference/reference_markers.fasta -out GCA_009379975.1_ASM937997v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 09:02:55,473] [INFO] Task succeeded: Blastn
[2023-06-17 09:02:55,478] [INFO] Selected 32 target genomes.
[2023-06-17 09:02:55,478] [INFO] Target genome list was writen to GCA_009379975.1_ASM937997v1_genomic.fna/target_genomes.txt
[2023-06-17 09:02:55,519] [INFO] Task started: fastANI
[2023-06-17 09:02:55,519] [INFO] Running command: fastANI --query /var/lib/cwl/stg537c468b-6ab9-4536-91f3-0d8e99d39f36/GCA_009379975.1_ASM937997v1_genomic.fna.gz --refList GCA_009379975.1_ASM937997v1_genomic.fna/target_genomes.txt --output GCA_009379975.1_ASM937997v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 09:03:35,266] [INFO] Task succeeded: fastANI
[2023-06-17 09:03:35,267] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c0d1aa7-57fa-4e97-9125-42a28bc96776/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 09:03:35,267] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c0d1aa7-57fa-4e97-9125-42a28bc96776/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 09:03:35,294] [INFO] Found 32 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 09:03:35,295] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 09:03:35,295] [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
Haloechinothrix halophila	strain=YIM 93223	GCA_000504245.1	1069073	1069073	type	True	80.2578	720	1428	95	below_threshold
Thermocrispum municipale	strain=DSM 44069	GCA_000427825.1	37926	37926	type	True	79.2934	498	1428	95	below_threshold
Amycolatopsis albispora	strain=WP1	GCA_003312875.1	1804986	1804986	type	True	79.0236	608	1428	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	78.9566	572	1428	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	78.9212	571	1428	95	below_threshold
Amycolatopsis magusensis	strain=DSM 45510	GCA_017875555.1	882444	882444	type	True	78.8475	603	1428	95	below_threshold
Amycolatopsis thermoflava	strain=N1165	GCA_000473265.1	84480	84480	type	True	78.8393	591	1428	95	below_threshold
Amycolatopsis methanolica	strain=239	GCA_000371885.1	1814	1814	type	True	78.7978	577	1428	95	below_threshold
Amycolatopsis anabasis	strain=EGI 650086	GCA_009765355.1	1840409	1840409	type	True	78.7851	617	1428	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	78.7843	584	1428	95	below_threshold
Amycolatopsis methanolica	strain=239	GCA_000739085.1	1814	1814	type	True	78.7228	590	1428	95	below_threshold
Amycolatopsis alkalitolerans	strain=SYSUP0005	GCA_006152065.1	2547244	2547244	type	True	78.6682	510	1428	95	below_threshold
Amycolatopsis cihanbeyliensis	strain=DSM 45679	GCA_006715045.1	1128664	1128664	type	True	78.6318	539	1428	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	78.6305	547	1428	95	below_threshold
Prauserella aidingensis	strain=DSM 45266	GCA_024171865.1	387890	387890	type	True	78.5537	449	1428	95	below_threshold
Amycolatopsis balhimycina	strain=DSM 44591	GCA_000384295.1	208443	208443	type	True	78.5029	595	1428	95	below_threshold
Amycolatopsis sulphurea	strain=DSM 46092	GCA_002564045.1	76022	76022	type	True	78.4824	449	1428	95	below_threshold
Amycolatopsis lexingtonensis	strain=DSM 44653	GCA_014873755.1	218822	218822	type	True	78.4601	625	1428	95	below_threshold
Amycolatopsis lexingtonensis	strain=NRRL B-24131	GCA_002156005.1	218822	218822	type	True	78.4316	568	1428	95	below_threshold
Amycolatopsis saalfeldensis	strain=DSM 44993	GCA_900110575.1	394193	394193	type	True	78.4228	549	1428	95	below_threshold
Amycolatopsis vastitatis	strain=H5	GCA_002234595.1	1905142	1905142	type	True	78.4094	603	1428	95	below_threshold
Amycolatopsis tolypomycina	strain=DSM 44544	GCA_900105945.1	208445	208445	type	True	78.3903	591	1428	95	below_threshold
Prauserella rugosa	strain=NRRL B-2295	GCA_000719975.1	43354	43354	type	True	78.3706	447	1428	95	below_threshold
Haloechinothrix aidingensis	strain=YIM 98757	GCA_013450155.1	2752311	2752311	type	True	78.3599	468	1428	95	below_threshold
Prauserella rugosa	strain=DSM 43194	GCA_007829565.1	43354	43354	type	True	78.3527	458	1428	95	below_threshold
Saccharomonospora halophila	strain=8	GCA_000383775.1	129922	129922	type	True	78.3388	362	1428	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	78.3299	601	1428	95	below_threshold
Amycolatopsis nivea	strain=CFH S0261	GCA_004522235.1	1644109	1644109	type	True	78.3093	542	1428	95	below_threshold
Saccharomonospora iraqiensis	strain=IQ-H1	GCA_000430445.1	52698	52698	type	True	78.302	412	1428	95	below_threshold
Saccharomonospora xinjiangensis	strain=XJ-54	GCA_000258175.1	75294	75294	type	True	77.981	367	1428	95	below_threshold
Saccharothrix texasensis	strain=DSM 44231	GCA_003752005.1	103734	103734	type	True	77.8419	485	1428	95	below_threshold
Saccharothrix obliqua	strain=SC076	GCA_019375475.1	2861747	2861747	type	True	77.6247	439	1428	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 09:03:35,297] [INFO] DFAST Taxonomy check result was written to GCA_009379975.1_ASM937997v1_genomic.fna/tc_result.tsv
[2023-06-17 09:03:35,298] [INFO] ===== Taxonomy check completed =====
[2023-06-17 09:03:35,298] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 09:03:35,298] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c0d1aa7-57fa-4e97-9125-42a28bc96776/dqc_reference/checkm_data
[2023-06-17 09:03:35,299] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 09:03:35,347] [INFO] Task started: CheckM
[2023-06-17 09:03:35,347] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009379975.1_ASM937997v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009379975.1_ASM937997v1_genomic.fna/checkm_input GCA_009379975.1_ASM937997v1_genomic.fna/checkm_result
[2023-06-17 09:04:13,555] [INFO] Task succeeded: CheckM
[2023-06-17 09:04:13,557] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-17 09:04:13,583] [INFO] ===== Completeness check finished =====
[2023-06-17 09:04:13,583] [INFO] ===== Start GTDB Search =====
[2023-06-17 09:04:13,584] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009379975.1_ASM937997v1_genomic.fna/markers.fasta)
[2023-06-17 09:04:13,584] [INFO] Task started: Blastn
[2023-06-17 09:04:13,584] [INFO] Running command: blastn -query GCA_009379975.1_ASM937997v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c0d1aa7-57fa-4e97-9125-42a28bc96776/dqc_reference/reference_markers_gtdb.fasta -out GCA_009379975.1_ASM937997v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 09:04:15,299] [INFO] Task succeeded: Blastn
[2023-06-17 09:04:15,304] [INFO] Selected 19 target genomes.
[2023-06-17 09:04:15,304] [INFO] Target genome list was writen to GCA_009379975.1_ASM937997v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 09:04:15,337] [INFO] Task started: fastANI
[2023-06-17 09:04:15,337] [INFO] Running command: fastANI --query /var/lib/cwl/stg537c468b-6ab9-4536-91f3-0d8e99d39f36/GCA_009379975.1_ASM937997v1_genomic.fna.gz --refList GCA_009379975.1_ASM937997v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009379975.1_ASM937997v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 09:04:37,763] [INFO] Task succeeded: fastANI
[2023-06-17 09:04:37,780] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 09:04:37,780] [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_009379975.1	s__Amycolatopsis_C sp009379975	100.0	1412	1428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis_C	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009377395.1	s__Amycolatopsis_C sp009377395	80.7514	735	1428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377475.1	s__Amycolatopsis_C sp009377475	80.3121	732	1428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000504245.1	s__Amycolatopsis_C halophila	80.2491	721	1428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000427825.1	s__Thermocrispum municipale	79.3128	496	1428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Thermocrispum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016464705.1	s__Saccharomonospora sp016464705	79.0631	576	1428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003312875.1	s__Amycolatopsis albispora	79.0222	610	1428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003001955.1	s__Saccharomonospora shujinwangii	78.9087	580	1428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017875555.1	s__Amycolatopsis magusensis	78.8827	598	1428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017309385.1	s__Amycolatopsis sp017309385	78.7981	636	1428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765355.1	s__Amycolatopsis anabasis	78.7705	619	1428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000739085.1	s__Amycolatopsis methanolica	78.7608	585	1428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	96.3446	100.00	100.00	1.00	1.00	2	-
GCF_006152065.1	s__Amycolatopsis alkalitolerans	78.6452	513	1428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018885265.1	s__Amycolatopsis_D sp018885265	78.6347	545	1428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105945.1	s__Amycolatopsis tolypomycina	78.3771	593	1428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013450155.1	s__Haloechinothrix aidingensis	78.3258	474	1428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Haloechinothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719975.1	s__Saccharomonospora rugosa	78.3186	453	1428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	99.54	99.08	0.98	0.95	3	-
GCF_000258175.1	s__Saccharomonospora xinjiangensis	77.9998	366	1428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	96.93	96.93	0.94	0.94	2	-
GCA_009379845.1	s__Tamaricihabitans sp009379845	77.4772	410	1428	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Tamaricihabitans	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 09:04:37,782] [INFO] GTDB search result was written to GCA_009379975.1_ASM937997v1_genomic.fna/result_gtdb.tsv
[2023-06-17 09:04:37,783] [INFO] ===== GTDB Search completed =====
[2023-06-17 09:04:37,789] [INFO] DFAST_QC result json was written to GCA_009379975.1_ASM937997v1_genomic.fna/dqc_result.json
[2023-06-17 09:04:37,789] [INFO] DFAST_QC completed!
[2023-06-17 09:04:37,789] [INFO] Total running time: 0h1m58s